To remove variants that encode for PE-PPE proteins from .vcf file

Question

[kumari.indu31]

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 intersect -u -a R883.vcf -b pe_ppe.bed > R883_no_PE.vcf

The output file is fine, however when we are using Annovar, to obtain the file for further analysis using command:

table_annovar.pl R883.vcf -buildver MTB -out R883_anno -remove -protocol refGene -operation g -nastring . --vcfinput

In the final annotated file, we are observing PE and PPE proteins. Can someone give a solution to this problem?

[Pierre Lindenbaum]

vcftools is deprecated. how about getting the complement of pe_ppe.bed with bedtools complement and then just use:

bcftools view --targets-file not-pe-ppe.bed  R883_Filter.vcf > R883_no_PE.vcf

[husensofteng]

It is not very clear what is the content of pe_ppe.bed. In case you want to exclude variants that overlap regions in the pe_ppe.bed file you can simply use intersectBed with the -v flag.

[kumari.indu31]

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.

[Kevin Blighe]

Please show the entries from ANNOVAR. They could be referring to upstream and downstream of the gene. Removing variants from a VCF is as simple as bcftools view --exclude

[kumari.indu31]

We did removed proteins using bcftools view --exclude, however, after running Annovar, we are facing same problem.

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[Kevin Blighe]

You did not quite answer my question:

Please show the entries from ANNOVAR.