search

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
7 stars 7 forks source link

Updated pipeline/samtools combo produces empty vcf output #108

Open ybolon-nmdp opened 9 years ago

ybolon-nmdp commented 9 years ago

mpileup for variant output command probably needs fixing

ghost commented 9 years ago

The mpileup calls are currently commented out https://github.com/nmdp-bioinformatics/pipeline/blob/master/process_fastq.bash#L156

ybolon-nmdp commented 9 years ago

Appears the general tools are not updated locally, only by those who do so individually (my run appears correct, Marina's is not)