Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Converting VCF to PLINK PED format, need help? ketan_bnf Bioinformatics 2 03-21-2017 01:35 AM
Converting VCF to GFF (again) francois.sabot Bioinformatics 3 08-24-2016 03:48 AM
converting from Annovar to VCF kjaja Bioinformatics 1 12-14-2011 06:24 PM
converting vcf between different assemblies krawitz Bioinformatics 1 05-03-2011 09:26 AM
need help with converting VCF to GTF/GFF format rudi283 Bioinformatics 4 03-05-2011 10:49 AM

Thread Tools
Old 06-19-2012, 06:31 AM   #1
Location: New Jersey, USA

Join Date: May 2011
Posts: 17
Exclamation Converting .sam to .vcf

I have some files in the .sam format which I obtained after I ran Stampy on some Cancer reads. I now have to convert the .sam files to .vcf files to do some analysis and am clueless on how to do the conversion. Any help or hints would be much appreciated.
bnfoguy is offline   Reply With Quote
Old 06-19-2012, 06:46 AM   #2
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 700

Use samtools with mpileup and use bcftools command:
samtools and bcftools are part of the samtools collection.
PLEASE DO examine the options to each command and understand them.

samtools mpileup -R -d 1000 -l rangehg18.chr -uf hg18.fa test.bam | bcftools view -g - > test.vcf

additional note: you will want to convert your sam into a sorted bam ("test.bam" in the example above)

Last edited by Richard Finney; 06-19-2012 at 07:34 AM.
Richard Finney is offline   Reply With Quote

conversion, read, read mapping, sam file, vcf

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 09:17 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO