Hi Wolfgang,
AFAIK, samtools can only call short variants (SNPs / indels), despite the
fact that you'll see evidence in the raw mpileup format. I think you'd need
to use something like BreakDancer, DELLY, or even SGA's graph-diff tool
(I'm experimenting with this for longer insertions, but don't have any
conclusions yet.
Others probably have better suggestions; this isn't an area I know very
well ...
~Joe
On Tue, Jun 3, 2014 at 3:48 AM, Wolfgang Maier <
[email protected]> wrote:
> I can provide a bit more details to my question. I've
> managed to create bam
> input that gives rise to the following mpileup output:
>
> [snip]
>
> chrX 8982279 g 10 .......... EJIJJJJC;J
> chrX 8982280 a 10 .......... DHJJJJJ@HJ
> chrX 8982281 a 10 .......... DHHJJJJIBI
> chrX 8982282 a 10 .......... DHHHJJJIEJ
> chrX 8982283 a 10 .......... DHHGHJJHEJ
> chrX 8982284 a 10 .......... DHHHHHJHIJ
> chrX 8982285 c 10 .......... DFHHHHHFIJ
> chrX 8982286 g 10 .......... DFFHHHGCGJ
> chrX 8982287 c 10 .......... DFFFHHH:HJ
> chrX 8982288 a 10 .......... DFFFFHHDBH
> chrX 8982289 g 10 .......... DFFFFFHFDH
> chrX 8982290 a 10
>
> .-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTT
>
> TCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACC
>
> AGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTT
>
> TGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGG
>
> CCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAG
>
> GAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGAT
>
> GAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGA
>
> GGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATAT
>
> CGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTA
>
> AGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGG
>
> AACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATTTTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG.-
>
> 1241CAACGTAAGATTTAAAACATGACTCGTTGCGAACCTCGATCAATGTCGGCTGCGCGATTTTTTCAAAGCTTATTATTTGATACTCACTATCAGGAAAGCAGTACGCAGGAAAGCAACACATTATGAAAATATTTAGAAAATGAGATTTGTGATTGAACCACATAAAACATTCAATTTCATAAACATAAATTATTTATTAAACTATCAACGTACAACAGCAATAACATTTTTGAAGATTGGAACTATAATTGGCTTTACTTGGATTTTCTCTATCCTTTGTGCTATGCCCTTTGCGATCCATCACCGAGCCGATTACATTATGAAAAGCTGGCCAGGGACAGACAACAGAATACCGGTAAAATAGAGTTTATTGACAATAACTCAGCAAAGTCTTTTAAGGTTAAATCTTCAAAAATGTGCATGATAGCAGTGATGTTTGAACCAAAGCTAGCGTCAACTTTTAAGGTAGTTAATAAATAAAAATTATCTTATACAGGGTGCAAGTTTGTATATTTTTTTCAGATTCTATTTCACTTCTCTGCCATAGCATTCTTTGCACTCCCACTGTTTACAATTGTAATTCTCTATGCAAGAATTGCATGTAAGGTAAGAAAAGTTGAACGGTGAAAAGCAAATTTTAAATTCACATTAAAACATTGATTGTTTTAAAATGAACGTTTTAATATCGTAATGAATAACGGATACACGTAAAACAAAAATTAAACAAAAACTCACCTGTTCTTTCATTTAGGTATCCAGCAACAGAACAATTCAACCAGGCGAACTTGATATCACTGAGGAACTGCAAATGAGAATCAATGCAATTTTATGTGAGTTCGGGATGAGTTGTTGATAAAAAACAGATGTAGGAGGGGTAGAAAATTGGAAAGTGAGGAACCGAATATGGGAGGGATTGGAGCGGAAAACGAATGCGTGAGCAGAGACTAGAAATGGATGTACTTAGATGAAGTACAAACTATCGTATTGTTCCATACAATTTTCAGTGGATATTTTTGTATT
>
> TTTCGGAATTTCGAGAACTGCGGTAGTTTATTGTTTAGTAACAGAGTTTTTAGTAACAAAGAGTAGAAACAAGGTAAAGTGACAATTTATGCAAATTTTGGGTTTTCTGGATGAATACTGTTTTTCACTTTAACTGTTATATTTTGTCACTACAGATAAAATATTGTATGTTCCCAAAAAGTGAGAAAAATATGAGCACATTTTGTCATTGTCTAGTGGCG
> DCFFFFFHHH
> chrX 8982291 c 10 ********** DCCFFFFDDH
> chrX 8982292 a 10 ********** DCCFFFFDDH
> chrX 8982293 a 10 ********** DCCFFFFDDH
> chrX 8982294 c 10 ********** DCCFFFFDDH
> chrX 8982295 g 10 ********** DCCFFFFDDH
> chrX 8982296 t 10 ********** DCCFFFFDDH
> chrX 8982297 a 10 ********** DCCFFFFDDH
> chrX 8982298 a 10 ********** DCCFFFFDDH
> chrX 8982299 g 10 ********** DCCFFFFDDH
> chrX 8982300 a 10 ********** DCCFFFFDDH
> chrX 8982301 t 10 ********** DCCFFFFDDH
> chrX 8982302 t 10 ********** DCCFFFFDDH
> chrX 8982303 t 10 ********** DCCFFFFDDH
> chrX 8982304 a 10 ********** DCCFFFFDDH
> chrX 8982305 a 10 ********** DCCFFFFDDH
> chrX 8982306 a 10 ********** DCCFFFFDDH
> chrX 8982307 a 10 ********** DCCFFFFDDH
> chrX 8982308 c 10 ********** DCCFFFFDDH
> chrX 8982309 a 10 ********** DCCFFFFDDH
> chrX 8982310 t 10 ********** DCCFFFFDDH
> chrX 8982311 g 10 ********** DCCFFFFDDH
> chrX 8982312 a 10 ********** DCCFFFFDDH
> chrX 8982313 c 10 ********** DCCFFFFDDH
> chrX 8982314 t 10 ********** DCCFFFFDDH
> chrX 8982315 c 10 ********** DCCFFFFDDH
> chrX 8982316 g 10 ********** DCCFFFFDDH
> chrX 8982317 t 10 ********** DCCFFFFDDH
> chrX 8982318 t 10 ********** DCCFFFFDDH
> chrX 8982319 g 10 ********** DCCFFFFDDH
> chrX 8982320 c 10 ********** DCCFFFFDDH
> chrX 8982321 g 10 ********** DCCFFFFDDH
> chrX 8982322 a 10 ********** DCCFFFFDDH
> chrX 8982323 a 10 ********** DCCFFFFDDH
> chrX 8982324 c 10 ********** DCCFFFFDDH
> chrX 8982325 c 10 ********** DCCFFFFDDH
> chrX 8982326 t 10 ********** DCCFFFFDDH
> chrX 8982327 c 10 ********** DCCFFFFDDH
> chrX 8982328 g 10 ********** DCCFFFFDDH
> chrX 8982329 a 10 ********** DCCFFFFDDH
> chrX 8982330 t 10 ********** DCCFFFFDDH
> chrX 8982331 c 10 ********** DCCFFFFDDH
> chrX 8982332 a 10 ********** DCCFFFFDDH
>
> [/snip]
>
> indicating a 1241bp deletion on chrX (actually, this is
> C.elegans data).
>
> However, when I do genotype calling on the same bam input
> using
>
> samtools mpileup -r chrX:8900000-9000000 -Dgu -f
> WS220.64_chr.fa input.bam |
> bcftools view -gv - > output.vcf
>
> then that deletion is totally ignored (I tried already -
> with no effect -
> disabling BAQ calculation and -Q 0 just to make sure those
> aren't the problem).
>
> I am just looking for an explanation for this behavior and,
> ideally, a
> solution that allows me to keep using samtools for aligned
> input like this.
>
> The thought behind this is that I would like to stick with
> one variant
> caller for everything (SNVs, indels, deletions) instead of
> invoking
> different ones for every variant type.
>
> Any thoughts?
>
> Wolfgang
>
>
> Wolfgang Maier <wolfgang.maier <at>
> biologie.uni-freiburg.de> writes:
>
> >
> > I'm currently experimenting with split-reads alignment to
> detect
> > deletions in WGS data and I'm wondering whether samtools
> mpileup
> > combined with bcftools is able to call larger deletions
> (typically
> > several hundred bases) as opposed to just small indels
> when presented
> > with appropriately aligned reads.
> > From a first test with samtools 0.1.19 and engineered
> bam data
> > simulating a 1.4 kb deletion the answer seems to be no,
> but I'd be
> > grateful for any help or explanation why it can't work.
> >
> > Thanks a lot,
> > Wolfgang
> >
>
>
>
> ------------------------------------------------------------------------------
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>
--
Joseph Fass
Lead Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
[email protected]
phone ~ 530.752.2698
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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