HI:
I used samtools mpileup to to find mutations. My sample genome is relative small and the coverage is about 1000X (illumina paired-end 90bp)
I used following code to generate VCF:
samtools view -bS sample.sam > sample.bam#generate bam
samtools sort sample.bam sample.sorted.bam#sort bam
samtools mpileup -ugf sample.fas sample.sorted.bam | bcftools view -vcg > sample.vcf#generate VCF file
In my vcf output, There are just two mutations, but I visulized the sam file in IGV and found lots of mutations. I supposed those mutations is filter out because of bad qc, So I used "-Q 0 -q 0 -C 0" but no more mutations were found.
Are there other parameters I didn`t found?
Any sugestions will be appreciated!
I used samtools mpileup to to find mutations. My sample genome is relative small and the coverage is about 1000X (illumina paired-end 90bp)
I used following code to generate VCF:
samtools view -bS sample.sam > sample.bam#generate bam
samtools sort sample.bam sample.sorted.bam#sort bam
samtools mpileup -ugf sample.fas sample.sorted.bam | bcftools view -vcg > sample.vcf#generate VCF file
In my vcf output, There are just two mutations, but I visulized the sam file in IGV and found lots of mutations. I supposed those mutations is filter out because of bad qc, So I used "-Q 0 -q 0 -C 0" but no more mutations were found.
Are there other parameters I didn`t found?
Any sugestions will be appreciated!
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