Different total of SNPs and Indels after selection

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10.5 years ago

widya.angelica • 0

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.

HaplotypeCaller GATK • 2.3k views

ADD COMMENT • link updated 3.2 years ago by Ram 44k • written 10.5 years ago by widya.angelica • 0

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Could you provide the commands that you used to split the variants and to count them?

ADD REPLY • link updated 3.2 years ago by Ram 44k • written 10.5 years ago by Paweł Sztromwasser ▴ 10

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Hi, Pawel.

I used the SelectVariants tool (-T SelectVariants) and -selectType INDEL for INDEL calling or -selectType SNP for 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.

ADD REPLY • link updated 3.2 years ago by Ram 44k • written 10.5 years ago by widya.angelica • 0

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