Question

Allele count from BAM file

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5.3 years ago

mona11224 • 0

How to get reference and alternate allele count from BAM file at a given chromosomal position?

next-gen sequencing SNP • 2.3k views

ADD COMMENT • link updated 5.3 years ago by Gabriel R. ★ 2.9k • written 5.3 years ago by mona11224 • 0

score 0 · Answer 1 · 2019-08-16

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5.3 years ago

GouthamAtla 12k

ADD COMMENT • link 5.3 years ago by GouthamAtla 12k

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I dont have VCF file have only .bam file and in that file chromosomal position is specified EX: chr12:6789007

ADD REPLY • link 5.3 years ago by mona11224 • 0

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If you have reference genome, generate a VCF file from your positions of interest or call SNPs from your bam file and then calculate allele counts.

ADD REPLY • link 5.3 years ago by GouthamAtla 12k

score 0 · Answer 2 · 2019-08-16

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5.3 years ago

Gabriel R. ★ 2.9k

It is one line in glactools:

glactools  bam2acf [reference].fa [iinput].bam  sampleid  |  glactools  view - |cut -f 1-3,6

In the last column, the format is REF,ALT:cpg

Be aware that it filters out reads marked as QC failed and PCR duplicates.

ADD COMMENT • link 5.3 years ago by Gabriel R. ★ 2.9k