Hello,
file.sam
#I convert SAM to BAM
#I sort BAM file
I remove duplicat, then I detect variants with samtools mpileup
I obtain no errors, bcf file contain data. (file is about gigabase). => samtools mpileup generates an empty output.
When I convert bcf into vcf, I obtain
and different lines with
but the vcf file only contains the header and this line :
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT srt_file.bam
#convert bcf into vcf
Someone can help me?
Thanks in advance
file.sam
#I convert SAM to BAM
Code:
samtools view -bS file -o file.bam
Code:
samtools sort file.bam file.srt
Code:
samtools mpileup -uf genome.fasta srt_file.bam | bcftools view -bvcg - > file_raw.bcf
When I convert bcf into vcf, I obtain
Code:
[mpileup] 1 samples in 1 input files <mpileup> Set max per-sample depth to 8000
Code:
[bcfview] 434500000 sites processed. [afs] 0:54828.077 1:20102.090 2:25069.833 [bcfview] 434600000 sites processed. [afs] 0:44750.569 1:24548.359 2:30701.072
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT srt_file.bam
#convert bcf into vcf
Code:
bcftools view file_raw.bcf | vcfutils.pl varFilter -D100 > variant.flt.vcf
Thanks in advance
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