Variant calling analysis
I am trying to filter a VCF file so that the filtered file has a VAF of less than 50% and a depth of at least 200 for variant supporting bases. The output VCF file should be sorted by chromosome and should retain the VCF header, so that it can be used as input for other tools that accept VCF files.
So far, I have tried running this code using Pandas library, but that only resulted in an empty dataframe.
Could you please let me know what I am doing wrong?
Thank you so much!
I am also attaching the format of my VCF file here.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Re-format sample columns in VCF file
written by phinguyen •
-
Error: Require Genotypes in VCF file in order to output IMPUTE format.
written by Warrenkb •
-
Why am I getting only one common value when comparing two excel files?
written by namck •
-
How to convert a FASTQ file to FASTA file without the number of reads
written by sabreenaalam12345 •
-
BEDOPS convert2bed output
written by nehaklkn •
-
Variant Effect Predictor (VEP) warning on insertions: coordinates are not (start = end + 1)
written by beketamas •
-
gsea msigdb RNA-seq input file
written by biology_inform •
-
Saving file as .vcf
written by Maryam •
-
Resistome Analyzer Report
written by Bio_Crap •
-
Calculation of VAF (variant allele frequency)
written by JJ
Did you try
bcftools view?E.g.,
Or, use
SnpEffNote: This is just an example I did not test the command myself.
There must be tools which would do the job easily, but I was just wondering if I could do that using Python.
There are already Python packages for that, as an example cyvcf2