Parsing VCF Data
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
• 1,676 views
•
link
updated
by
Ram
•
written
by
gcooper1245 •
•
written
by
gcooper1245 •
2 answers
bcftools annotate
Usage: bcftools annotate [options] <in.vcf.gz>
(...)
--rename-chrs <file> rename sequences according to map file: from\tto
• 0 views
•
link
written
by
Pierre Lindenbaum
Version: 1.9 (using htslib 1.9)
• 0 views
•
link
written
by
Pierre Lindenbaum
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?
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.
Log in to answer this question.
More posts like this
-
My VCF file structure is strange and less compatible to data processing programs.
written by kgwkk2 •
-
Issue with VCF format while using Pharmcat
written by taniamahmood38 •
-
Linkage disequilibrium from VCF file of variants in bacterial metagenomes
written by matthias.hotzinger •
-
GATK GenotypeGVCFs output is empty gvcf file
written by GK1610
