Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Odd behavior using samtools mpileup, bcftools JimC Bioinformatics 7 05-21-2013 12:34 PM
Samtools mpileup/bcftools cristae8 Bioinformatics 3 05-02-2012 01:43 PM
samtools mpileup and bcftools command lines to compare individual differences? aslihan Bioinformatics 1 11-17-2011 03:20 PM
Conflict between mpileup/bcftools and GATK in VCF file ericarcher Bioinformatics 0 09-25-2011 05:33 PM
questions about samtools mpileup & bcftools chenjy Bioinformatics 0 07-26-2011 05:21 AM

Thread Tools
Old 02-03-2011, 09:47 PM   #1
Junior Member
Location: Columbus, OH

Join Date: Nov 2010
Posts: 6
Default samtools mpileup and bcftools not reporting dbSNP ids

The vcf output after running mpileup and bcftools seems to fail to report dbSNP ids. Here are the commands I used against my BAM file...pretty much identical to the example code provided with the mpileup documentation.

samtools mpileup -ugf /data/genomes/hg19/hg19.fa aln.bam > aln_varRaw.bcf
bcftools view -cvg aln_varRaw.bcf | varFilter -D100 > aln.vcf

And here are the first 10 lines of the output vcf file.

chr1 16571 . G A 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,0,1;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 74817 . G A 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,0,1;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 118617 . T C 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,1,0;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 231504 . G A 23.8 . AF1=1.000;AFE=0.829;DP4=0,0,2,0;MQ=30 PL:GT:GQ 55,6,0:1/1:49
chr1 232960 . C A 11.1 . AF1=1.000;AFE=0.768;DP4=0,0,0,2;MQ=30 PL:GT:GQ 42,6,0:1/1:49
chr1 233473 . C G 4.13 . AF1=0.500;AFE=0.307;DP4=1,1,2,0;MQ=30;PV4=1,0.0048,1,0.23 PL:GT:GQ 32,0,48:0/1:35
chr1 235976 . C A 52 . AF1=1.000;AFE=0.899;DP4=0,0,2,1;MQ=30 PL:GT:GQ 84,9,0:1/1:63
chr1 726481 . T G 13.9 . AF1=1.000;AFE=0.799;DP4=0,0,2,0;MQ=30 PL:GT:GQ 45,6,0:1/1:49
chr1 726939 . G C 14.9 . AF1=1.000;AFE=0.806;DP4=0,0,1,1;MQ=30 PL:GT:GQ 46,6,0:1/1:49
chr1 726944 . C G 21.8 . AF1=1.000;AFE=0.827;DP4=0,0,1,1;MQ=30 PL:GT:GQ 53,6,0:1/1:49

I realize that these 10 calls may not have a match in dbSNP but NONE of my calls have an associated rsID. rsID should be listed in the 3rd column.

I looked for specific parameters for setting up a connection to dbSNP but I cannot seem to find that information. Seems like I'm missing something.
dmb is offline   Reply With Quote
Old 02-04-2011, 07:14 AM   #2
Senior Member
Location: Germany

Join Date: May 2010
Posts: 101

The tools you're using just report the SNPs found in your data. You'll have to assign the SNPs the dbSNP data with another tool, e.g. GATK VariantAnnotator, to which you provide the dbSNP entries as a file.
epigen is offline   Reply With Quote
Old 08-13-2012, 11:18 PM   #3
Junior Member
Location: Shenzhen, China

Join Date: Aug 2012
Posts: 3

So ga...I thought it can conect with dbSNP.
lanzz is offline   Reply With Quote

dbsnp, mpileup, samtools, snp calling

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 08:29 AM.

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