I'll definitely check that out. I sorted the bam to see if that fixed the problem (no luck) but perhaps they are sorted differently.
The only reason I think this might not fix things is because, without the vcftools.pl varFilter step, there are SNPs called across all chromosomes. The information seems to be in order in the .bcf file...it's just not getting through the filtering step.
Thank you for the response!
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First thing to check...I wonder if one file is sorted chr1, chr2, chr3...and the other chr1, chr10, chr11...
That discrepancy might explain why the file stops at Chr1.
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Missing chromosomes in vcf output
**UPDATE**
Problem solved. The local version of the .fai index file I was using only contained chromosome 1. Version on the server that I accidentally checked multiple times was fine. Whoops.
Hello everyone!
I have bam files for several histone ChIP-seq and RNA-seq experiments and I am attempting to call SNPs. I used the following command successfully with the ChIP-seq data:
Code:samtools mpileup -uD -f hg19.fa INPUT.bam | bcftools view -bcvg - > INPUT_raw.bcf; bcftools view DL237_INPUT_raw.bcf | vcfutils.pl varFilter -D100 > INPUT.vcf;
Code:samtools mpileup -uD -f Homo_sapiens.GRCh37.72.dna_rm.toplevel.fa.gz RNA.bam | bcftools view -bcvg - > RNA_raw.bcf; bcftools view RNA_raw.bcf | vcfutils.pl varFilter -D100 > RNA.vcf;
The output VCF starts out just like all the others but doesn't have entries for any chromosomes except for chromosome 1.
If I take out the vcfutils.pl varFilter step and run:
Code:samtools mpileup -uD -f Homo_sapiens.GRCh37.72.dna_rm.toplevel.fa.gz RNA.bam | bcftools view -bcvg - > RNA_raw.bcf; bcftools view RNA_raw.bcf > RNA.vcf;
Last edited by spyf89; 08-13-2014, 07:01 AM.
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