Hi all,
When I tried to call variants by 25 BAM files like this,
$ samtools mpileup -P ILLUMINA -ugf hg19.fasta *.bam | bcftools view -bcvg - > var.raw.bcf ; bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
Then the standard output was
[mpileup] 25 samples in 25 input files
<mpileup> Set max per-file depth to 320
[afs] 0:0.000 1:0.000 2:0.000 3:0.000 4:0.000 5:0.000 6:0.000 7:0.000 8:0.000 9:0.000 10:0.000 11:0.000 12:0.000 13:0.000 14:0.000 15:0.000 16:0.000 17:0.000 18:0.000 19:0.000 20:0.000 21:0.000 22:0.000 23:0.000 24:0.000 25:0.000 26:0.000 27:0.000 28:0.000 29:0.000 30:0.000 31:0.000 32:0.000 33:0.000 34:0.000 35:0.000 36:0.000 37:0.000 38:0.000 39:0.000 40:0.000 41:0.000 42:0.000 43:0.000 44:0.000 45:0.000 46:0.000 47:0.000 48:0.000 49:0.000 50:0.000
and the program just stopped, the VCF file just only had the header information. I don't why, could you help me?
thanks
When I tried to call variants by 25 BAM files like this,
$ samtools mpileup -P ILLUMINA -ugf hg19.fasta *.bam | bcftools view -bcvg - > var.raw.bcf ; bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
Then the standard output was
[mpileup] 25 samples in 25 input files
<mpileup> Set max per-file depth to 320
[afs] 0:0.000 1:0.000 2:0.000 3:0.000 4:0.000 5:0.000 6:0.000 7:0.000 8:0.000 9:0.000 10:0.000 11:0.000 12:0.000 13:0.000 14:0.000 15:0.000 16:0.000 17:0.000 18:0.000 19:0.000 20:0.000 21:0.000 22:0.000 23:0.000 24:0.000 25:0.000 26:0.000 27:0.000 28:0.000 29:0.000 30:0.000 31:0.000 32:0.000 33:0.000 34:0.000 35:0.000 36:0.000 37:0.000 38:0.000 39:0.000 40:0.000 41:0.000 42:0.000 43:0.000 44:0.000 45:0.000 46:0.000 47:0.000 48:0.000 49:0.000 50:0.000
and the program just stopped, the VCF file just only had the header information. I don't why, could you help me?
thanks
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