User: kumari.indu31

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Posts by kumari.indu31

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Comment: A: To remove variants that encode for PE-PPE proteins from .vcf file
... We did removed proteins using bcftools view --exclude, however, after running Annovar, we are facing same problem. ...
written 12 weeks ago by kumari.indu310
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Comment: A: To remove variants that encode for PE-PPE proteins from .vcf file
... We have tried this command as well: bcftools view --targets-file not-pe-ppe.bed R883_Filter.vcf > R883_no_PE.vcf However, when we annotate file using annovar then we are still finding PE-PPE genes in the final plot. ...
written 12 weeks ago by kumari.indu310
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To remove variants that encode for PE-PPE proteins from .vcf file
... We re trying to remove PE-PPE proteins from filtered .vcf file using the following commands: intersectBed -a R883_Filter.vcf -b pe_ppe.bed -header > output.vcf vcftools --vcf R883.vcf --exclude-positions-overlap pe_ppe_pos.txt --recode --recode-INFO-all --out R883_pos.vcf bedtools ...
bedtools annovar vcftools written 12 weeks ago by kumari.indu310

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