SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools mpileup unexpected behaviour CHRYSES Bioinformatics 4 06-19-2012 06:19 AM
strange results of samtools liying Bioinformatics 3 09-22-2011 11:02 PM
BWA behaviour with Mate Pair data + Multi read mapping apratap Bioinformatics 5 06-23-2011 04:38 PM
Strange behavior of BWA xinwu Bioinformatics 0 12-07-2010 04:57 PM
behaviour of bwa mapping for homologous regions. KevinLam Bioinformatics 1 07-28-2010 08:39 AM

Reply
 
Thread Tools
Old 04-12-2011, 05:15 AM   #1
francesconea
Junior Member
 
Location: Milano

Join Date: Apr 2011
Posts: 5
Default strange bwa/samtools behaviour (?)

Hello everyone
First of all, I'd like to thank you for this super-useful community everyone's contributing to build up. It's a kind of next-gen sequencing for me
Now, coming to my question:
I'm quite new in next-gen sequencing and I'm working with Illumina data (paired-end, 76bp long reads, whole exome) and I cannot have any of my aligned bam/sam files with header included. That is, I have all the pretty @SQ lines and @PG line at the end of the header. What I can't gain is the @HD/tVN/SO line at the very beginning of the header.

In addiction, if i try to do
bwa aln - bwa sampe - samtools view - samtools sort in a separate way, when I try to give a look to my new-beautiful-bam-file's header I'll receive always this message:

samtools view -H prova.bam <- my command
[bam_header_read] EOF marker is absent.

while, when I sort it, I get this other one:
samtools sort prova.bam prova_sorted <- my command

[bam_header_read] EOF marker is absent. The input is probably truncated.

All of this doesn't happen at all if I do that in a piped way...even if the @HD/tVN:/tSO line is still missing

Any ideas would be particularly appreciated
__________________
wherever you go, whatever you do, always bring a bioinformatic with you

Last edited by francesconea; 04-12-2011 at 05:16 AM. Reason: wanted to better check posting options
francesconea 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 04:51 AM.


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