How can I convert the following .vcf data into a pandas dataframe? enter link description here Source: Python..
I’m new in python and is not my domain but I need to work on this for my project : I have a VCF file annotated with Annovar and it is a result of a comparison between family members data, and after I grepped the information related to commons variants using Grep and I obtained ..
I have this file with fragments like this: ## many comments here chrY 2893596 . C T . PASS AC=1;AN=32183;AF=3.10723e-05;popmax=afr;strings1;strings2;strings2;strings3;etc;ENSG00000129824|strings|strings|strings|intron_variant|MODIFIER|HSFY3P|ENSG00000227289|Transcript|morestrings|etc|||||||||||||||||| chrY 2893598 . A G . PASS AC=1;AN=32183;AF=3.10723e-05;popmax=afr;strings1;strings2;strings2;strings3;etc;ENSG00000129824|strings|strings|strings|upstream_gene_variant|MODIFIER|HSFY3P|ENSG00000227289|Transcript|morestrings|etc|||||||||||||||||| The thing is that column 8 consists from row of many strings, enclosed with either ";" or pipes. I try to write Python code that counts type ..
Is it possible to check if the ALT field in VCF is an angle bracketed token or a list of angle bracketed tokens using the pyvcf python package? For example, consider the following VCF row: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12877_S1 22 42523949 . T < CN0 >,< CN2 >,< CN3 ..
I have about 200 files having long header lines that starts with "#" and then records with 4 columns like the following: file_1.vcf ##some_comments that span many lines ##some_comments that span many lines #CRHOM POS REF ALT chr1 111 A G chr2 222 G T chrY 99999 A C file_2.vcf ##some_comments that span many lines ..
I’m trying to compare a line in one file and put every matching line in another file in an output file. For example here is the first file. chr8 18 . T T * * chr8 29 . C T . . chr9 21 . TA T . . chr18 22 . C T . ..