Hi all,
This is my framework to call SNP from 50 fastq files,
1> use bowtie to get SAM from fastq. reference genome: hg19.fa, paras in bowtie: -k 2 -v 2. Then I have 50 SAM files
2> convert SAM to BAM. cmd line: samtools view -bS s01.sam > s01.bam, then I have 50 BAM files
3> sort BAM. cmd line: samtools sort s01.bam > s01.sort.bam
4> convert 50 sorted BAM files to one vcf file.
cmd line:
samtools mpileup -P ILLUMINA -ugf hg19.fa *.sort.bam | bcftools view -bcvg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
However, the quality of VCF file seems not good. I'm wondering that in which step can I do the quality control? thanks very much
This is my framework to call SNP from 50 fastq files,
1> use bowtie to get SAM from fastq. reference genome: hg19.fa, paras in bowtie: -k 2 -v 2. Then I have 50 SAM files
2> convert SAM to BAM. cmd line: samtools view -bS s01.sam > s01.bam, then I have 50 BAM files
3> sort BAM. cmd line: samtools sort s01.bam > s01.sort.bam
4> convert 50 sorted BAM files to one vcf file.
cmd line:
samtools mpileup -P ILLUMINA -ugf hg19.fa *.sort.bam | bcftools view -bcvg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
However, the quality of VCF file seems not good. I'm wondering that in which step can I do the quality control? thanks very much
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