SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MiSeq pipeline, per-genome bam vs per chromosome bam & vcf swNGS Bioinformatics 1 03-29-2012 05:00 AM
Counting entries in bam-files: difficulties with samtools and bamToBed Azazel Bioinformatics 4 01-17-2011 07:31 PM
BFast index creation & other SOLiD difficulties keebs42 Bioinformatics 9 02-09-2010 08:13 PM
sff_extract and ssaha2 problem facing edge Bioinformatics 4 10-01-2009 05:11 PM
MIRA3: setup BAMBUS Configuration File problem facing edge Bioinformatics 0 10-01-2009 01:43 AM

Reply
 
Thread Tools
Old 04-04-2013, 03:57 PM   #1
leftisthominid
Member
 
Location: Florida

Join Date: Apr 2013
Posts: 13
Default Trying to get Altai Neanderthal chromosome 2 VCF, facing difficulties

Hello, I am trying to generate a vcf file from http://cdna.eva.mpg.de/neandertal/al...1000g.2.dq.bam

I have downloaded it to the University of Florida's Fisher Bioinformatics cluster as Neanderthal.bam

I've used the following command to successfully sort it
/sandbox/gms6231/PROGRAMS/samtools sort Neanderthal.bam Neanderthal_sort

and I've been able to get a bcf file out of it as such
/sandbox/gms6231/PROGRAMS/samtools mpileup -f hg19_chr2.fa Neanderthal_sort.bam >Neanderthal.bcf

but as I try to generate my vcf file with this command
/sandbox/gms6231/PROGRAMS/bcftools view -cvg Neanderthal.bcf > Neanderthal.vcf

I begin to get this error:
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000
Neanderthal.out (END)

What I am I doing wrong?

Thanks!
leftisthominid is offline   Reply With Quote
Reply

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 06:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO