get unwanted allele in ALT column

[jiehuichen]

Hi Xianjie,

Thanks for this great software for SNP calling.

With --genotype option specified, I found one of the SNP with Allele we did not want.

As the attached sheet shows, the REF is G, and the ALT is T, but the allele we want is A.

How could I get the information for the allele we want? Do I need to provide the custom vcf to get A listed in the ALT column?

Thanks a lot,

Best,
Jiehui
cellSNP_1.cells.xlsx

[hxj5]

Hi Jiehui,

Yes, you may set specific allele in REF/ALT column of custom VCF to get its information (using -R or -T option in mode 1), I assume you genotyped in mode 2 (i.e., denovo genotyping without input VCF).

Best,
Xianjie

[jiehuichen]

Many thanks.

Follow your comment, I did it with the customized VCF using -R in mode 1.

Great software!