Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
hisat2 file reads don't match up ronaldrcutler RNA Sequencing 19 06-21-2016 12:04 PM
variant calling on a subsample of a BAM file.. batman Bioinformatics 5 11-11-2015 12:23 AM
Does anybody know how to convert dbsnp to .vcf (variant calling format)? alexbmp Bioinformatics 13 04-05-2015 11:24 PM
Extract reference and aligned sequences from BAM file basing on VCF file floem7 Bioinformatics 3 01-19-2015 04:08 AM
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 01:16 PM

Thread Tools
Old 05-05-2017, 09:06 AM   #1
Junior Member
Location: US

Join Date: May 2017
Posts: 1
Default Variant calling: reference positions with no reads don't appear in vcf file


I mapped my reads back to a reference genome using BWA-mem and now I'm using the bcftools mpileup/call/filter pipeline to obtain variant calls. I was converting my vcf files to fasta sequences for each of my individuals, masking non-called and filtered sites (./.) with Ns. However, I noticed that reference positions to where no reads where mapped in the original bam do not appear in any of my bcf or vcf files. For example, in my chromosome 1, since no reads mapped from position 1 to 100, my vcf file will start in position 1:100, and not 1:1. Therefore, when I use bcftools consensus, I get these positions as reference calls and not as Ns (which I wanted, because they don't have support in my data).

Shouldn't all positions in the genome appear in the bcftools mpileup output and not only those where reads mapped? Is there a way I can generate vcfs will all the positions in the genome?

Thank you
MattRSmith is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:40 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO