I followed the GATK pipeline.
when I use the IGV to see the bam file I found the question:
position chr17:7578524 : G(51 reads)-A(20 reads) I think this is a snp, but the position doesn't exist the result VCF files. GATK don't think this is a snp,even in lowQual snp.
why? the position have so high sequencing deepth.Who can explain it
when I use the IGV to see the bam file I found the question:
position chr17:7578524 : G(51 reads)-A(20 reads) I think this is a snp, but the position doesn't exist the result VCF files. GATK don't think this is a snp,even in lowQual snp.
why? the position have so high sequencing deepth.Who can explain it
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