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Old 12-06-2010, 05:26 PM   #1
Ling1
Junior Member
 
Location: Vancouver

Join Date: Dec 2010
Posts: 1
Default samtools mpileup

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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Old 05-24-2012, 10:09 AM   #2
yina
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Location: Cuernavaca, México

Join Date: Jul 2009
Posts: 6
Default

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