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
Thanks in advance for any help!!
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