Hi everyone,
When I try mpileup in samtools-0.1.12.
There is segfault:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
Segmentation fault
Also, I tried
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!
When I try mpileup in samtools-0.1.12.
Code:
samtools-0.1.12/samtools mpileup -C50 -gf ref.fasta file.bam > file.bcf
[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
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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