Adding a fake genotype column to a vcf file

jweger1988

Member

Join Date: Apr 2017
Posts: 37

Adding a fake genotype column to a vcf file

11-29-2017, 02:29 PM

Hello all!

I need to add a fake genotype column to my vcf files produced with lofreq in order to use them with vcf tools for specific analyses. Can anyone help me with this?

Here is an example of the vcf produced with lofreq

Code:

##fileformat=VCFv4.0
##fileDate=20171129
##source=lofreq call -f JW316_consensus.fa -o 316.vcf 316.sorted.bam 
##reference=JW316_consensus.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
pJW316-17_beforeNGS	102	.	A	C	69	PASS	DP=373;AF=0.061662;SB=2;DP4=329,21,23,0
pJW316-17_beforeNGS	110	.	A	C	96	PASS	DP=396;AF=0.065657;SB=3;DP4=343,26,26,0
pJW316-17_beforeNGS	114	.	C	A	105	PASS	DP=417;AF=0.052758;SB=4;DP4=364,31,22,0
pJW316-17_beforeNGS	117	.	T	G	78	PASS	DP=420;AF=0.047619;SB=0;DP4=361,31,19,1
pJW316-17_beforeNGS	173	.	A	C	79	PASS	DP=703;AF=0.041252;SB=13;DP4=581,90,29,0
pJW316-17_beforeNGS	175	.	A	C	88	PASS	DP=701;AF=0.041369;SB=16;DP4=573,93,29,0
pJW316-17_beforeNGS	183	.	A	C	99	PASS	DP=664;AF=0.048193;SB=24;DP4=517,112,32,0
pJW316-17_beforeNGS	239	.	A	C	129	PASS	DP=720;AF=0.054167;SB=14;DP4=446,231,32,7
pJW316-17_beforeNGS	249	.	A	C	104	PASS	DP=739;AF=0.050068;SB=26;DP4=458,239,33,4
pJW316-17_beforeNGS	300	.	A	C	136	PASS	DP=664;AF=0.058735;SB=32;DP4=251,373,27,12
pJW316-17_beforeNGS	305	.	A	C	98	PASS	DP=742;AF=0.043127;SB=3;DP4=253,447,14,18
pJW316-17_beforeNGS	316	.	T	G	91	PASS	DP=775;AF=0.046452;SB=10;DP4=201,525,5,31
pJW316-17_beforeNGS	320	.	T	G	81	PASS	DP=760;AF=0.043421;SB=10;DP4=188,530,4,29

Thanks in advance for any help!!

Tags: bioinformatics, ngs, vcf

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