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It's been a while since I've worked with samtools, but I think I'm up to par on how the new samtools/bcftools work. I've got some aligned RNA-seq data that I'm trying to call the consensus sequence for. I'm able to generate the VCF just fine, but once I pipe it into vcfutils.pl vcf2fq everything explodes. I just get a whole bunch of lines saying 'nnnnnnnnnnnnnnn'. This is samtools 0.1.18 r982 (latest) on a Ubuntu 11.10 64-bit system with Perl 5.12.4. Any idea as to what might be going wrong?
This is my command line:
~/bin/samtools mpileup -r chr6:44328750-44328835 -f hg18.fasta -u GSE25840_GSM424320_GM06985_gencode_spliced.sorted.bam | ~/bin/bcftools view -cg - | ~/bin/vcfutils.pl vcf2fq
This is my command line:
~/bin/samtools mpileup -r chr6:44328750-44328835 -f hg18.fasta -u GSE25840_GSM424320_GM06985_gencode_spliced.sorted.bam | ~/bin/bcftools view -cg - | ~/bin/vcfutils.pl vcf2fq
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