samtools mpileup

Ling1

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Join Date: Dec 2010

Posts: 1
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#1

samtools mpileup

12-06-2010, 06:26 PM

Hi everyone,

When I try mpileup in samtools-0.1.12.

Code:

samtools-0.1.12/samtools mpileup -C50 -gf ref.fasta file.bam > file.bcf

There is segfault:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
Segmentation fault

Also, I tried

Code:

samtools-0.1.12/samtools mpileup -ugf file.fasta file.bam | samtools-0.1.12/bcftools/bcftools view -bvcg - > var.raw.bcf samtools-0.1.12/bcftools/bcftools view var.raw.bcf | samtools-0.1.12/bcftools/vcfutils.pl varFilter -D100 > var.flt.vcf awk '{print $1}' var.flt.vcf | sort | uniq -c

The output after awk was:
12111 10
1640 11
1 #CHROM
1 ##fileformat=VCFv4.0

Can anyone give me some hints on what the problem is? Thank you!
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yina

Junior Member

Join Date: Jul 2009

Posts: 6
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#2

05-24-2012, 10:09 AM

Hi I have the same problem, did you found the solution?? any hint would help
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