error when running samtools mpileup and bcftools

[linp5]

Hi all

I run the code below which is modified from [1]

samtools mpileup -uf wg.fa ERR000589.srt.bam | /home/linp/linpDisk4/DataSeq/bcftools/bcftools call -mv -Oz

But I encounter such a error:

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[vcf.c:753 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is supported.
Failed to open: -

but I can successfully run samtools mpileup separately:
samtools mpileup -f wg.fa ERR000589.srt.bam > ERR000589.bcf

the ERR000589.bcf file looks as:
chr10 60173 T 1 ^Z. H
chr10 60174 T 1 . H
chr10 60175 G 0
chr10 60176 G 1 . /
chr10 60177 G 1 . I
chr10 60178 T 1 . .
chr10 60179 T 1 . 8
chr10 60180 G 1 . G
chr10 60181 G 1 . I

Could anyone please give me some tips about what happened?


[1] https://github.com/samtools/bcftools/wiki/HOWTOs

[dpryan]

Try:

 samtools mpileup -ugf wg.fa ERR000589.srt.bam | /home/linp/linpDisk4/DataSeq/bcftools/bcftools call -mv -Oz

[linp5]

Thank you dpryan!

But the problem still exists:

linp@wuserver:~/linpDisk4/DataSeq$ samtools mpileup -ugf wg.fa ERR000589.srt.bam | /home/linp/linpDisk4/DataSeq/bcftools/bcftools call -mv -Oz
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[vcf.c:753 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is supported.
Failed to open: -

[dpryan]

My only guess is that you have different versions of samtools and bcftools (make sure you're using the tagged 1.0 version of both if you got this from github). If that's not the case and no one else is able to give you an answer here then you should post this to the samtools-help email list.

[linp5]

Thank you dpryan!

the versions are:

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 1.0-15-gc15888a (using htslib 1.0-2-g1903fd4)
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd


Do you think they are in-compatible ?

[dpryan]

Ah, yeah, you need to either use the version of bcftools that came with samtools 0.1.19 or use the newer version of samtools available here.