Nickier
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Activity overview
Latest activity by Nickier-
Nickier commented,
Great! Thank you @Genevieve Brandt (she/her) very much~
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Nickier commented,
Hi Genevieve Brandt (she/her) , I used SelectVariants and got the single sample vcf from the multi-sample vcf. Maybe I need to filter out some mutations, for example, GT tag is ./. , 0/0 .
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Nickier commented,
Hi Pamela Bretscher, Of course, I got a MAF file output by Funcotator, which looks like this
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Nickier commented,
Hi Pamela Bretscher, In fact, I first use SelectVariants to split the multi-sample vcf file into single-sample vcf, and then filter out the sites with GT tags of 0/0, 0|0 and ./. in the single-samp...
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Nickier commented,
Hi, Pamela Bretscher , Thank you, I am hesitating how to convert multiple sample vcf files to maf. I will try the method you mentioned
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Nickier commented,
Hi Genevieve Brandt (she/her) , How to split a multi sample VCF with GATK or shell script such as awk ?
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Nickier created a post,
Annotation of multi-sample vcf and conversion to maf format
After running the GVCF mode and VQSR, I get a multi-sample vcf file. How do I continue processing, such as VEP annotation, to get a maf file? The purpose of my analysis is to screen for tumor susc...
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Nickier commented,
Hi Alex Falconer , Thanks a lot~ I will have a try.
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Nickier commented,
Hi, I will call vcf in the deep seqeuncing data ( 10,000x coverage ) with Mutect2. Should I set --max-reads-per-alignment-start 0 ?
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Nickier commented,
Hello! Could you improve a readme file to introduct the resource files?