A question about BED file and finding mutation in vcf file

Question

[Zahra]

Hi all,

I have a vcf file and to separate my interest gene I have used a BED file that has been downloaded from UCSC. Here is the location of the gene in the BED file :

chr7    140433812   140624564   uc003vwc.4  0   -   140434396   140624503   0   18  758,135,132,119,47,177,85,118,137,37,160,120,149,103,104,264,102,199,   0,5799,15274,19262,20174,42899,43978,47563,49008,53535,60295,66349,67399,73947,74879,100596,116098,190553,

And I have a mutation in my vcf file that is located exactly in this gene:

7   14046760    .   G   A   .   PASS    PoN_remove=False;Validation_Method=none;sequencer=Illumina_GAIIx;Validation_Status=Untested;tumor_f=0.340909;source=WGS;Strand=+;status=Somatic;init_t_lod=36.374381;Center=broad.mit.edu;t_lod_fstar=37.376344;judgement=KEEP;NCBI_Build=37;phase=Phase_I  GT:alt_count:ref_count  ./.:15:29

But when I have used vcftools, it could't find this mutation:

vcftools --vcf  /input.vcf/ --out /output.vcf/ --bed /Bed_file.bed/  --recode-INFO-all --recode

I don't know what is the problem and how to fix it. Is special preprocessing necessary?something like adding dictionary?

Thanks for any help.

[raphael.B]

Unless there is a typo, your mutation does not fall in your gene. Regardless of it be careful with chromosome names when using a bed file to subset a VCF. Here your chromosome is named 7 in your bed but chr7 in your vcf.

[Zahra]

It worked! The problem was the chr and number of digits. Thank you and ATpoint

[ATpoint]

As said here: How to subset the mutations that occur just in my interest genes within the vcf file? use tabix and if that does not work then either the mutation does not overlap (here it doesn't, the BED coordinates have 9 digits, the VCF coordinate has 8 so this is hopefully not a typo as noted already) or chromosome identifiers are not the same (also not the case here 7 vs chr7).