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Different total Indel and SNPs after selection

gisv71gisv71 SingaporeMember

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.

Best Answer

Answers

  • gisv71gisv71 SingaporeMember

    Hi, Sheila.

    Exactly like you said, the sites are all mixed SNP/indel.
    Thank you so much for your answer.
    GBU.

    Kindest regards,
    Angelica

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