search

FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
51 stars 19 forks source link

N-masking human genome #62

Closed parichitran closed 2 years ago

parichitran commented 2 years ago

Dear Felix, I want to N-mask my Grch-38 reference genome at heterozygous SNP position

I have a VCF file generated from Whole Genome Sequencing of my cell line data with GATK-4.

But SNP split N-masks my homozygous SNPs from my VCF file.

will it be fine regarding my case

FelixKrueger commented 2 years ago

Hi @parichitran

If you wanted to use SNPsplit for the the human genome you would indeed have to modify the genome preparation script to mask heterozygous positions instead of homozygous calls.

I have never used it myself yet, but alternative (and probably very useful approach) could be haplotype phasing your SNPs: https://whatshap.readthedocs.io/en/latest/

parichitran commented 2 years ago

Thanks a lot for your speedy reply Felix.I got cleared now.