Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Adding a fake genotype column to a vcf file

    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!!

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin


    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
    Yesterday, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
55 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X