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
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
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