samtools mpileup

[Ling1]

Hi everyone,

When I try mpileup in samtools-0.1.12.

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

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!

[yina]

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