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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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About the SNP result #37

Open hmyh1202 opened 5 years ago

hmyh1202 commented 5 years ago

I have do some test using the software and get much more snp site than that using GATK. And many snps are consecutive, can you give me some advice for using that software.

tamsen commented 5 years ago

Hi there,

GATK is typically for germline calling and Pisces by default is somatic, so generally GATK is looking for variants with frequency 20% and up (usually well above the noise of the system), and Pisces is looking for variants with frequency 1% and up (much closer to the noise of the system). Pisces generally expects pretty clean bams - otherwise its hard to discriminate tumor from noise. So yes - its going to call a lot more variants.

If you are getting a suspicious amount of consecutive SNPs, Pisces is probably exposing a lot of poor alignments in your bam. You might want to consider troubleshooting the source of the poor alignments. Depending on the SNPs calls made (an abundance of Gs? or more like white noise.?) and the positions of the SNPs (always at the end of the reads?) or does your aligner have a really high gap penalty? In any case, it is probably worth looking into and resolving at the BAM-level.

best Tamsen