Parsing VCF Data

Question

[gcooper1245]

So I have about 150 of these VCF files and I forgot to parse the reference before running all 150. For downstream analysis with snpEff, I need to have the chromsome ID only contain JTAI01000001 -> JTAI01000053 in that collumn, not all that other junk. Does anyone have a way in which I could potentially substitute out everything but the middle JTAI01000001 part of these GVCF's so I can proceed with my analysis.

##contig=<ID=ENA|JTAI01000001|JTAI01000001.1,length=360176>
##contig=<ID=ENA|JTAI01000002|JTAI01000002.1,length=959544>
##contig=<ID=ENA|JTAI01000003|JTAI01000003.1,length=208220>
##contig=<ID=ENA|JTAI01000004|JTAI01000004.1,length=470636>
##contig=<ID=ENA|JTAI01000005|JTAI01000005.1,length=225370>
##contig=<ID=ENA|JTAI01000006|JTAI01000006.1,length=364413>
##contig=<ID=ENA|JTAI01000007|JTAI01000007.1,length=1279890>
##contig=<ID=ENA|JTAI01000008|JTAI01000008.1,length=18993>
##contig=<ID=ENA|JTAI01000009|JTAI01000009.1,length=291696>
##contig=<ID=ENA|JTAI01000010|JTAI01000010.1,length=821>
##contig=<ID=ENA|JTAI01000011|JTAI01000011.1,length=128648>
##contig=<ID=ENA|JTAI01000012|JTAI01000012.1,length=66483>
##contig=<ID=ENA|JTAI01000013|JTAI01000013.1,length=592675>
##contig=<ID=ENA|JTAI01000014|JTAI01000014.1,length=1554>
##contig=<ID=ENA|JTAI01000015|JTAI01000015.1,length=3499>
##contig=<ID=ENA|JTAI01000016|JTAI01000016.1,length=5436>
##contig=<ID=ENA|JTAI01000017|JTAI01000017.1,length=1198>
##contig=<ID=ENA|JTAI01000018|JTAI01000018.1,length=6108>
##contig=<ID=ENA|JTAI01000019|JTAI01000019.1,length=9709>
##contig=<ID=ENA|JTAI01000020|JTAI01000020.1,length=523589>
##contig=<ID=ENA|JTAI01000021|JTAI01000021.1,length=97817>
##contig=<ID=ENA|JTAI01000022|JTAI01000022.1,length=268453>
##contig=<ID=ENA|JTAI01000023|JTAI01000023.1,length=215216>
##contig=<ID=ENA|JTAI01000024|JTAI01000024.1,length=79716>
##contig=<ID=ENA|JTAI01000025|JTAI01000025.1,length=121647>
##contig=<ID=ENA|JTAI01000026|JTAI01000026.1,length=31279>
##contig=<ID=ENA|JTAI01000027|JTAI01000027.1,length=3130>
##contig=<ID=ENA|JTAI01000028|JTAI01000028.1,length=340737>
##contig=<ID=ENA|JTAI01000029|JTAI01000029.1,length=5801>
##contig=<ID=ENA|JTAI01000030|JTAI01000030.1,length=4981>
##contig=<ID=ENA|JTAI01000031|JTAI01000031.1,length=318753>
##contig=<ID=ENA|JTAI01000032|JTAI01000032.1,length=45350>
##contig=<ID=ENA|JTAI01000033|JTAI01000033.1,length=114418>
##contig=<ID=ENA|JTAI01000034|JTAI01000034.1,length=1682>
##contig=<ID=ENA|JTAI01000035|JTAI01000035.1,length=28211>
##contig=<ID=ENA|JTAI01000036|JTAI01000036.1,length=117188>
##contig=<ID=ENA|JTAI01000037|JTAI01000037.1,length=188157>
##contig=<ID=ENA|JTAI01000038|JTAI01000038.1,length=3440>
##contig=<ID=ENA|JTAI01000039|JTAI01000039.1,length=373676>
##contig=<ID=ENA|JTAI01000040|JTAI01000040.1,length=996>
##contig=<ID=ENA|JTAI01000041|JTAI01000041.1,length=618>
##contig=<ID=ENA|JTAI01000042|JTAI01000042.1,length=211284>
##contig=<ID=ENA|JTAI01000043|JTAI01000043.1,length=87165>
##contig=<ID=ENA|JTAI01000044|JTAI01000044.1,length=873289>
##contig=<ID=ENA|JTAI01000045|JTAI01000045.1,length=795>
##contig=<ID=ENA|JTAI01000046|JTAI01000046.1,length=590>
##contig=<ID=ENA|JTAI01000047|JTAI01000047.1,length=705>
##contig=<ID=ENA|JTAI01000048|JTAI01000048.1,length=1262>
##contig=<ID=ENA|JTAI01000049|JTAI01000049.1,length=1307>
##contig=<ID=ENA|JTAI01000050|JTAI01000050.1,length=766>
##contig=<ID=ENA|JTAI01000051|JTAI01000051.1,length=795>
##contig=<ID=ENA|JTAI01000052|JTAI01000052.1,length=724>
##contig=<ID=ENA|JTAI01000053|JTAI01000053.1,length=619>
##reference=file:///scratch/gwc32007/crypto_genomes/30976_hominis_genome.fasta
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  ERR1305010
 ENA|JTAI01000001|JTAI01000001.1    1   .   A   <NON_REF>   .   .   END=2   GT:DP:GQ:MIN_DP:PL   
 0:7:0:7:0,0
 ENA|JTAI01000001|JTAI01000001.1    3   .   A   <NON_REF>   .   .   END=3   GT:DP:GQ:MIN_DP:PL   
 0:7:99:7:0,298
 ENA|JTAI01000001|JTAI01000001.1    4   .   C   <NON_REF>   .   .   END=8   GT:DP:GQ:MIN_DP:PL   
 0:7:0:7:0,0
ENA|JTAI01000001|JTAI01000001.1 9   .   A   <NON_REF>   .   .   END=9   GT:DP:GQ:MIN_DP:PL   
0:7:99:7:0,300
ENA|JTAI01000001|JTAI01000001.1 10  .   C   <NON_REF>   .   .   END=11  GT:DP:GQ:MIN_DP:PL   
0:7:0:7:0,0
ENA|JTAI01000001|JTAI01000001.1 12  .   C   <NON_REF>   .   .   END=12  GT:DP:GQ:MIN_DP:PL   
0:7:99:7:0,284
 ENA|JTAI01000001|JTAI01000001.1    13  .   T   <NON_REF>   .   .   END=14  GT:DP:GQ:MIN_DP:PL   
0:7:0:7:0,0
 ENA|JTAI01000001|JTAI01000001.1    15  .   A   <NON_REF>   .   .   END=18  GT:DP:GQ:MIN_DP:PL   
0:7:99:7:0,276

Answer 1

[Pierre Lindenbaum]

bcftools annotate

Usage:   bcftools annotate [options] <in.vcf.gz>
(...)
       --rename-chrs <file>       rename sequences according to map file: from\tto

[Ram]

Pierre,

Which version do you see the from\tto description? The manual (both of them actually) says white-space separated.

[Pierre Lindenbaum]

Version: 1.9 (using htslib 1.9)

[Ram]

That's odd - the manual on htslib.org still says white space separated, but when I run bcftools annotate on my local machine, I see the from\tto. Could it be that the online manual is not being maintained properly?

Answer 2

[Ram]

This has been addressed multiple times on the forum. The best way to do this is to create a whitespace-separated file with new and old contig names like so:

ENA|JTAI01000001|JTAI01000001.1 JTAI01000001
ENA|JTAI01000002|JTAI01000002.1 JTAI01000002
..
..
ENA|JTAI01000053|JTAI01000053.1 JTAI01000053

and use that file with bcftools annotate --rename-chrs. See the bcftools manual to understand the exact syntax.