problems with bam file and mpileup

[Danielbenitezr]

Hello everyone:

I have a problem with samtools' mpileup.
Im trying to map a set of reads (only 1 library for now) against a reference genome, to find SNPs. The command line I used is:

$ samtools mpileup -uD -f ref_genome.fasta library.sorted.bam | bcftools view -bvcg library.raw.bcf

the output I get is this:

open: No such file or directory
[mpileup] 1 samples in 1 input files
Segmentation fault

i dont know what's wrong. I used this same command line with other data and it worked just fine, so I could use some help.

thank you!

[zhidkov.ilia]

Does "ref_genome.fasta" indexed?

-f FILE faidx indexed reference sequence file [null]

[Danielbenitezr]

yes, it is.

I run this command line earlier:

$ samtools faidx ref_genome.fasta

generating a ref_genome.fasta.fai file

I don´t think that's the problem =(

[Dethecor]

Fasta file chromosome names

Hi, can you post the result of:

grep ">" ref_genome.fasta

You can get these segfaults without message when your fasta header lines have spaces in them.

Cheers,
Paul

[Richard Finney]

Quick guess ...
Shouldn't it be
$ samtools mpileup -uD -f ref_genome.fasta library.sorted.bam | bcftools view -bvcg - > library.raw.bcf

[Danielbenitezr]

Thank you all!
actually it was the missing "- >" before the "library.raw.bcf"
thanks a lot!