Different total of SNPs and Indels after selection
Hi, I used HaplotypeCaller to call Indels and SNPs on my 30 samples and I separated the SNPs and Indels into 2 different files using SelectVariant tool.
I got 1954 SNPs and Indels in combination (in raw files), but after selection, I got only 277 indels and 1666 SNPs (in total only 1943, different from its raw file).
Why is it happening?
Many thanks before.
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widya.angelica •
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Could you provide the commands that you used to split the variants and to count them?
Hi, Pawel.
I used the
SelectVariantstool (-T SelectVariants) and-selectType INDELfor INDEL calling or-selectType SNPfor SNP calling. But, fortunately I have found the answer, the 11 missing samples were mixed Indel/SNP sites, so the tool could not determine and split them. Thanks anyway.