SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools faidx Segmentation fault baohua100 Bioinformatics 19 04-19-2016 07:09 AM
Segmentation fault with samtools rmdup Azazel Bioinformatics 1 09-05-2013 08:48 AM
Segmentation fault (core dumped) at contig step during SOAP denovo assembly tangzhonghui Bioinformatics 1 10-09-2012 05:32 PM
samtools mpileup segmentation fault adrian Bioinformatics 8 10-05-2012 07:17 AM
Segmentation fault (core dumped) in Samtools hanleng Bioinformatics 6 03-23-2012 02:42 PM

Reply
 
Thread Tools
Old 03-12-2012, 01:28 PM   #1
hanleng
Member
 
Location: Houston, TX

Join Date: Mar 2012
Posts: 15
Default Segmentation fault (core dumped) in Samtools

Hi, All,

I want to map the RNA-seq BMA files back to the reference, and I used the samtools pileup command. It always shows the error "Segmentation fault (core dumped)".

It should not be the problem in the reference genome, because I have tried "fold" command to format the reference genome, as well as the "faidx" in samtools. They did not work. Strangely, for different BAM files, the pileup sometimes shows the error at the very beginning, some times stopped at chr6, while some other times shows the errors at chr10 or later chromosomes.

My command is "samtools view -u Inputfile (BAM) | samtools pileup -vcf hg19.fa - > output". However, when I tried Partek, it runs very well.

Anyone has any idea what is the problem with these BAM files? What I should do to fix these bugs/modify the BAM files?

Thanks a lot.
hanleng 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 06:56 AM.


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