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Old 11-24-2011, 09:36 PM   #1
Location: shanghai

Join Date: Nov 2010
Posts: 24
Default SNP calling reads number

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
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Old 11-25-2011, 09:16 AM   #2
Location: Germany

Join Date: Mar 2011
Posts: 68

That could have many reasons. How are the mapping qualities of the reads at that position and how are the quality scores of the bp supporting the SNP?
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