周尤佳
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Latest activity by 周尤佳-
周尤佳 commented,
Hi Gökalp Çelik , Thank you for your help, i will consider filtering out low reads sites and calculate mutation rate at each mutation site that have higher reads in vcf to validate.
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周尤佳 commented,
Hi, Gökalp Çelik thanks for the advices. I added these 2 parameters and run again, and still get 965719 out of 1113553 passed filtration, also my rna-seq includes many intronic reads that I don't w...
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周尤佳 created a post,
About RNA seq snp filtration
REQUIRED for all errors and issues: a) GATK version used:v4.4.0.0 b) Exact command used: gatk VariantFiltration \ -R GRCh38.p14.genome.fa \ -V wt1.rdup.SNC.RG.filtered.vcf \ -O wt1.rdup.SNC...
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周尤佳 commented,
Hi Gökalp, Thanks for the help, I also want to know if Funcotator is designed to output snps presenting in the database only, because I found all my snps not in the database are filtered out or ju...
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周尤佳 created a post,
Funcotator log says "Cannot create complete funcotation for variant at chr1:25813992-25814012 due to alternate allele: *"
REQUIRED for all errors and issues: a) GATK version used:gatk-4.4.0.0 b) Exact command used:gatk Funcotator \ --variant /public/slst/home/lict/ZYJ/sladuk/gatk/filtered.I8_L1.rdup.SNC.RG.vcf \ ...