I am working on using bowtie and samtools to take a fastq file, map to HG19 using bowtie, and use samtools to find SNPs and output a VCF file.
I am able to get decent .vcf output, but the vcf file created has all 'N's for ref. Is there an easy fix?
I am using the commands:
bowtie -S humanref " + patfile + " > bw_out
samtools view -S -u bw_out > bw_bam
samtools sort bw_bam bw_bamsort
samtools mpileup -u -D bw_bamsort.bam > bcf_out
bcftools view bcf_out > vcf_out
Thanks!
I am able to get decent .vcf output, but the vcf file created has all 'N's for ref. Is there an easy fix?
I am using the commands:
bowtie -S humanref " + patfile + " > bw_out
samtools view -S -u bw_out > bw_bam
samtools sort bw_bam bw_bamsort
samtools mpileup -u -D bw_bamsort.bam > bcf_out
bcftools view bcf_out > vcf_out
Thanks!
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