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Old 06-24-2015, 08:28 AM   #1
Location: Quadraro, Rome

Join Date: Jul 2012
Posts: 11
Default GATK Haplotype Caller calls Indels in SOLID reads that IGV does not Display

Hello everyone,

I am Daniele and I'm a Junior Researcher in a private foundation in Rome.

Before explaining my problem, let me say that I am pretty new to the SOLID technology and to Variant Calling in general so forgive me if the question sounds dumb, but I couldn't find an answer nowhere!

That said, I am analyzing SOLID reads for a target resequencing experiments. The files were given me as BAM, already aligned to my reference genome using the lifescope suite provided by AB.

I used a classical approach for variant calling, so i preprocessed the reads, marked duplicates with Picard, and run the GATK pipeline using the Best Practices for Variant Calling (so I recalibrate the base QSs and I realigned around INDELS. ).

I have then used HaplotypeCaller for the variant calling and outputted the VCF files for my experiments.

Thing is that HaplotypeCaller does call several InDels that, when i check my final bam file (the one i give to Haplotype caller for calling variants) are not presents.

specifically, any InDel in my vcf is not seen in IGV, but some of them appears as single nucleotide variants when I unchecked the "Quality weight allele fraction" in the Alignment Panel inside the IGV preferences. I thought this was an IGV issue and played a little bit with the options, but I found no solution. Notably, the Genotype Quality of these position is always around 99 I checked around the web, but I cannot find any explanation to this behavior.

Can someone provide some help?

Thanks in advance!

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