hi,
I call variants using 'samtools mpileup' with parameter -l 'bed file' for
regions I need. However, For the same position (e.g. chrom 7 position 55242464
for hg19), which is included in two different bed files (one bigger, one
smaller), I have got different result: one with obviously INDEL in mpileup file
and Vcf file, one without.
What will be the reasons?
Looking forward to your help.
Thanks.
code:
samtools mpileup -l regions.bed -q 30 -Q 30 -L 10000 -C 50 -m 2 -F 0.002 -f
hg19.fasta bwa.bam > result.mpileup
version:
0.1.19-44428cd
Yang
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