Argonaut44
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Latest activity by Argonaut44-
Argonaut44 commented,
That was my mistake. I one book on bioinformatics I have read that the reference file should be the one vcf file mapped to. Thus, I did not properly read the original gatk documentation and got so ...
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Argonaut44 commented,
Thank you for the feedback. I will try the bcftools norm. Should I also create a custom h37d5_to_GRCh38 chain file or it is not an option?
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Argonaut44 created a post,
Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
Hi, I am using Picard LiftOverVCF 2.22.3 to liftover a VCF file (hs37d5 reference genome) to the GRCh38 genome using 21 chromosome of this VCF file as a toy dataset GRCh37_to_GRCh38 chain file VCF ...