Hi,
I have done a re-sequencing experiment to identify snps from candidate genes. I want to get a consensus sequence using BAM files generated by mapping reads with BWA. Ultimately I want to use the consensus fasta file in bedtools to get flanking sequences of SNPs. I have followed the commands suggested in the samtools help pages. These are the commands that I used for getting consensus fastq file.
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
I got the following message from vcfutils.pl and the output file contained mainly 'n's.
Use of uninitialized value $q in numeric lt (<) at /usr/bin/vcfutils.pl line 508, <> line 51404.
Use of uninitialized value $q in addition (+) at /usr/bin/vcfutils.pl line 518, <> line 51404.
Could any one please help me with this.
I have done a re-sequencing experiment to identify snps from candidate genes. I want to get a consensus sequence using BAM files generated by mapping reads with BWA. Ultimately I want to use the consensus fasta file in bedtools to get flanking sequences of SNPs. I have followed the commands suggested in the samtools help pages. These are the commands that I used for getting consensus fastq file.
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
I got the following message from vcfutils.pl and the output file contained mainly 'n's.
Use of uninitialized value $q in numeric lt (<) at /usr/bin/vcfutils.pl line 508, <> line 51404.
Use of uninitialized value $q in addition (+) at /usr/bin/vcfutils.pl line 518, <> line 51404.
Could any one please help me with this.
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