This doesn't seem to be implemented within mpileup. One could either re-write
those lines using a perl or awk script, or else disable split-read alignments
during the preceding read mapping.
- tom blackwell -
On Wed, 26 Aug 2015, ��˧ wrote:
Hi, Tom,
Sorry to bother you again. I have another question.
Following is one line from the result file of "samtools mpileup". Is there an option that could
filter the "reference skip" ('<' or '>') in the depth column?
chr10_C-T 3147419 G 7 <<,><>, ggggggg
For example, this is what I want:
chr10_C-T 3147419 G 2 ,, gg
Thanks!
-----原始邮件-----
发件人: "Thomas W. Blackwell" <[email protected]>
发送时间: 2015-08-20 21:25:48 (星期四)
收件人: "梁芳" <[email protected]>
抄送: [email protected], "李茹姣" <[email protected]>
主题: Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup
Might experiment with adding -A. I observe that one read pair has the
proper pair flag set (99,147) and the other pair has it unset (97,145).
The description for -A in the samtools 1.1 man page reads "Do not skip
anomalous read pairs in variant calling."
- tom blackwell -
On Thu, 20 Aug 2015, 温帅 wrote:
To whom it may concern,
I met a problem when using samtools-1.0 mpileup to deal with a pairend reads
mapping result file in sort bam format. The command I used was:
samtools mpileup -B -Q 0 -d 999999999 -f ref_all_C-T_G-A.fa mapping_ms.sort.bam
> mapping_ms.sort.bam.pile
Following are two paired reads from file "mapping_ms.sort.bam":
seq.5547# 97 chr10_C-T 292795 255 100M = 294319
1624
GTGATGAGTTGGAGTTGTATTAGTGTTTTTTATGAGAAGGGAGATTTTGGAAATTTAAGAATGATGATTGAGGTGAGGAAGAGGTAGAATTGAGTATTTT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:64G26T8
YS:i:0 YT:Z:DP NH:i:1
seq.5547# 145 chr10_C-T 294319 255 100M = 292795
-1624
TATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGTTAAGTGTTTTTTTATTAAGAATGTTGTATTGGAGTATTTAGAT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:-12
YT:Z:DP NH:i:1
seq.346110# 99 chr10_C-T 294276 255 100M = 294316
140
GAATTAGAGTTTGAAATAGAAGTAGTAAGTTTTAGTTAGGAAATATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:0 YT:Z:CP
NH:i:1
seq.346110# 147 chr10_C-T 294316 255 100M = 294276
-140
AAATATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGTTAAGTGTTTTTTTATTAAGAATGTTGTATTGGAGTATTTA
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:0 YT:Z:CP
NH:i:1
This is one line from the result file "mapping_ms.sort.bam.pile":
chr10_C-T 294382 T 1 , g
From the bam file we could easily know that for position "294382" the depth
should be 2 insead of 1. What options should I use if I don't want to filter any reads
when generated the result file?
Thanks very much for your time and I am looking forward to your reply.
Fang Liang
Beijing Institute of Genomics, Chinese Academy of Science
-----鍘熷閭欢-----
鍙戜欢浜� "Heng Li" <[email protected]>
鍙戦�佹椂闂� 2015-08-18 23:07:24 (鏄熸湡浜�)
鏀朵欢浜� "姊佽姵" <[email protected]>
鎶勯�� "鏉庤尮濮�" <[email protected]>
涓婚: Re: regarding to the result samtools mpileup
The first read is unpaired. mpileup doesn't use it by default. Please ask
[email protected] if you have further questions.
Heng
On Aug 18, 2015, at 5:14 AM, 姊佽姵 <[email protected]> wrote:
Dear Dr Li,
I met a problem when using samtools-1.0 mpileup to deal with a mapping result
file in sort bam format. The command I used is:
Following is the command I used to generate the mpileup file:
samtools mpileup -B -Q 0 -d 999999999 -f ref_all_C-T_G-A.fa mapping_ms.sort.bam
> mapping_ms.sort.bam.pile
This is part of the result file:
chr10_C-T 288153 A 1 . g
chr10_C-T 288154 T 1 . g
chr10_C-T 288155 T 1 . g
chr10_C-T 288156 A 1 . g
chr10_C-T 288157 G 1 . g
Here are two reads from the file mapping_ms.sort.bam from which we could see the depth
should be 2 for the above position "288155" instead of depth 1.
seq.197749# 153 2 chr10_C-T 288137 255 100M = 288137
0
GTTTGATGATTTTTTTATTAGAGATGTATGAAGTTTATTTTAAATTGGAAAAAAAAAATATATTATGTATTTAAGAATATGTTTTAAGATAAATTGTTTT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100YT:Z:UP NH:i:1
seq.11071# 99 1 chr10_C-T 288146 255 100M = 288392
346
TTTTTTTATTAGAGATGTATGAAGTTTATTTTAAATTGGAAAAAAAAAATATAGTATGTATTTAAGAATATGTTTTAAGATAAATTGTTTTTAGATATTT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:53T46 YS:i:-12
YT:Z:CP NH:i:1
What options should I use if I don't want to filter any reads when generated
the result file?
Thanks for your consideration!
鏉庡崥澹紝鎮ㄥソ锛屾垜鏄兂璇锋暀鎮ㄥ浣曟墠鑳借mpileup鐨勮緭鍑虹粨鏋滈噷鍚湁杈撳叆鏂囦欢鎵�鏈塺eads鐨勮鐩栧害淇℃伅锛屽氨鏄笉鎯宠繃婊ゆ帀浠讳綍涓�鏉ead.
Fang Liang
Beijing Institute of Genomics, Chinese Academy of Science
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