I got vcf file from my instructor. It is VEP annoted with over 50 options separated by ||. I noticed that the vcf is not arrange to appropriate columns so I decided to sort it.
I used this code to sort my vcf file according position:
$ grep "^#" input.vcf > output.vcf
$ grep -v "^#" input.vcf| sort -k1,1V -k2,2g >> output.vcf
However after I used it I expected to have output.vcf data sorted into columns. Instead all data of each variant data is still shift.
Am I doing something wrong? Is it different way to arrange vcf into columns?
1 answer
Rather than reinvent the wheel, use existing tools - bcftools sort, for example. Also, see this thread: https://bioinformatics.stackexchange.com/questions/6826/sort-vcf-by-contig-and-position-within-contig
Maybe -k2,2n would work better than -k2,2g in your solution.
It didn't even cross my mind. I guess it maybe the case. However I thought that when I use sort it sort the information according to my liking and arrange it into columns when I pipe it into a new vcf file. So my reasoning was that if the vcf will be sorted properly I would get even samples GT into separate columns. But still it queried with bcftool query into one chunk of information of samples GT. I really appreciate an hits because I am stuck with my main goal to separate samples GT into columns.
bcftools query is your friend when you want a table of comma/tab delimited values from a VCF file. You may also want to look into adding a column command to your pipe so it's easier to eyeball. See this post: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists where I describe how to use column to make things easier to look at.
Log in to answer this question.
-
Proper reanotation of genepanel with snpEff and dbNSFP
written by Lukas •
-
Using a Docker image with ensembl-vep
written by langziv •
-
Issue running VEP with GTF due to Tabix error
written by jensen.416 •
-
Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
written by maria2019
-
VEP is returning ClinVar fileds bank (-- custom annotation with VEP)
written by saadatagah.m •
-
How to remove duplicate SNP IDs from VCF files?
written by anikcropscience •
-
Grep VCF position awk
written by the_cowa •
-
Output going to stdout?
written by ForrestBear •
-
vcf2maf not generating `t_depth t_ref_count t_alt_count` columns in MAF file
written by Alejandro Jimenez Sanchez
-
How to sort a VCF file lexicographically by chromosome number?
written by Parth Patel •
Guys I am so sorry if this question is inappropriate but I started using linux half year ago.