Samtools call variant

[silasysh]

Hi,

I used samtools to call variant. I use the latest version 1.0. First, I have to generate bcf file. I run the following command.

samtools mpileup -t DP -ugf my.fasta my.bam

the result is always like this:

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Aborted

If I just run

samtools mpileup -f my.fasta my.bam

it works fine.

I have no idea what happens.

If I go back to use samtools-0.1.19 to run

samtools mpileup -uD -f my.fasta my.bam

everything is okay.

Could anyone helps me? Thank you.

Silas

[dpryan]

You're not doing anything obviously wrong. If you can share the BAM file (privately at least) then it'd be a good idea to post this on the samtools-help email list. There have been a few issues with the newest release that still need to get resolved and perhaps you've just found another one.

BTW, what happens if you just do the following with version 1.0:

 samtools mpileup -ugf my.fasta my.bam

I ask because that could help track down exactly where the problem is happening.

[silasysh]

Thank you.

If I just do the following:

samtools mpileup -ugf my.fasta my.bam

the result is like what I posted before. Nothing more.

I will try to post bam file to samtools-help email list. Thank you again.

Silas