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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Is there a good way to identify and add the gene names to the output vcfs? #113

Open pchatterjee7 opened 6 months ago

pchatterjee7 commented 6 months ago

Hi, Thank you for creating such a simple tool to work with. I have 1 vcf file for each of my samples. I want to add the gene names for the positions. I am trying bcftools annotate but it is not working. Any suggestion will be really helpful as I have a large number of samples. my current vcf format looks like this: #CHROM POS ID REF ALT QUAL FILTER INFO 1 632427 . T C . PASS AD=32;DP=32;OTH=8 1 1292517 . A G . PASS AD=0;DP=52;OTH=7 1 1888667 . A C . PASS AD=0;DP=21;OTH=6 1 2505339 . A G . PASS AD=0;DP=51;OTH=13 1 6079211 . T C . PASS AD=0;DP=41;OTH=37

hxj5 commented 6 months ago

Hi, you may look into this Biostars page "Addin gene information to VCF file", hope it can help.