User: jon.klonowski

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Posts by jon.klonowski

<prev • 15 results • page 1 of 2 • next >
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Answer: A: grep command on VCF
... The function works. The issue was something with the VCF file: unknown reason. bcftools view -i "controls_AF_popmax<0.5" input.vcf is the best answer if the VCF is formated corrected. Future people: Make sure your info field is formatted correctly. here I wanted the format liek this: > ...
written 8 weeks ago by jon.klonowski10
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Comment: C: BCFTools Query: Avoid grouping Alt Alleles
... I imagine iteratting over each sample would solve this bcftools query File_Name.vcf.gz -f'%CHROM\t %POS\t %ID\t %REF\t [%ALT]\n' | bgzip > output.txt.gz wrong ...
written 8 weeks ago by jon.klonowski10
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
... Looks like there were numerous extra info fields specified in the header that were not actually present. I just purged them, going to double check the header and try this all again. UPDATE: AFTER UPDATING INFO IT THE IT APPEARS TO BE WORKING. Lets see what I changed: 1. removed superfluous head ...
written 8 weeks ago by jon.klonowski10 • updated 7 weeks ago by finswimmer11k
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
... i will try to clean up my header completely and double check the positioning, maybe the annovar annotation didnt properly align the header and that is why i am getting the issue ...
written 8 weeks ago by jon.klonowski10
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Comment: C: grep command on VCF
... when i reintroduce the header and query the file, the controls_AF_popmax are all possible numbers between 1-NA ...
written 8 weeks ago by jon.klonowski10
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Comment: C: grep command on VCF
... This command is not functioning properly for me. We are talking about it on: https://www.biostars.org/p/375908/ ...
written 8 weeks ago by jon.klonowski10
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
... UPDATED VCF header where i deleted all the contig information and filtering information so it would fit in a single screenshot: PREVIOUS VCF HEADER https://ibb.co/rZRtR7F UPDATED VCF HEADER https://ibb.co/n8cWxm9 Sorry i am not sure the best way to share... and here is a record, not including sa ...
written 8 weeks ago by jon.klonowski10 • updated 7 weeks ago by finswimmer11k
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BCFTools Query: Avoid grouping Alt Alleles
... I am trying to query my vcf but I am running into a problem, the output looks like this: > chr17 61615660 chr17:61615660:T:TG,TC T TG,TC where the columns are >Chr Pos ID REF ALT and the line of code is: bcftools query File_Name.vcf.gz -f'%CHROM\t %POS\t %ID\t %REF\t %ALT\n' -i'GT="al ...
vcf 1000genomes bcftools annotation written 8 weeks ago by jon.klonowski10
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grep command on VCF
... Summery: my grep command is not working properly when applied to a vcf but worked fine on a dummy test file. The grep command is putting too many records.. I am trying to pull all records with 1000 Genomes AF < 0.5 from a vcf. the vcf is annotated and for each SNP the AF from 1KGenomes is unde ...
vcf grep bcf unix written 8 weeks ago by jon.klonowski10
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gatk SelectVariants odd behavior
... gatk SelectVariants is not working properly for me... I have a file of SNP ids (i.e chr1:861219:G:C) delimited with /n and a vcf where the snp ID is also formatted chr:pos:ref:alt (chr1:861219:G:C). The list file of SNPs were generated by subsetting a portion of the vcf SNPs (based on 1000G freque ...
selectvariants gatk vcf filtering snp written 8 weeks ago by jon.klonowski10 • updated 6 weeks ago by Biostar ♦♦ 20

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