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2.5 years ago
AndrMod
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I need to decorticate the #CHROM and #POS of a vcf, ie. to change them with new fields. I think I can arrange it on R.
But, before that, I must filter 500 variants out of 46K.
Some are just contigs, others are POS within a contig which don't suit our expectation. I have an idea of using vcftool for the latter task, but the panoply of commands (ancd required inputs) confuses me.
Can someone please shed me a light?
VCFtools sounds like a good approach. Can you clarify what filtering conditions you are looking to apply for the 500 variants you are interested in?
vcftools is deprecated. use bcftools
Simply the names of the #CHROM. They don't appear in the results of a BLAST. Same for some POS: some CHROM have POS which were not retrieved by BLAST.
Also, is there a way to do it on R?
what's the relation of a VCF with BLAST ? why don't you talk about BLAST in your initial question ? How can we know ??
The contigs-containing variants were BLASTed, sic simpliciter.
Some gave hits, some not.
Then I made some further filtering analyses based on the quality of the alignment.
that's not clear. show us an example.
CHROM 4920 has four variants: 456, 567, 678, 898:
CHROM_4920 _456 was retrieved by BLAST
CHROM_4920 _567 was not retrieved by BLAST
CHROM_4920 _678 was retrieved by BLAST
CHROM_4920 _898 was retrieved by BLAST