search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
224 stars 342 forks source link

Input file renaming #12

Closed sxv closed 8 years ago

sxv commented 8 years ago

I haven't noticed this before and I'm trying to figure out what is happening. A recent file that I'm processing with ANNOVAR is being renamed (filename is truncated) during processing, resulting in an unexpected output file name.

The command being run:

time perl /media/joannaprzybyl/4/software/annovar/table_annovar.pl \
    -vcfinput NPC.HK.12PY0019T-DNA.12PY0019-ensemble.temp3.vcf \
    /media/joannaprzybyl/4/software/annovar/humandb/ \
    -buildver hg19 \
    -out NPC.HK.12PY0019T-DNA.12PY0019-ensemble.temp3.vcf \
    -protocol refGene,ensGene,clinvar_20150330,popfreq_all_20150413,cosmic70,snp129,snp132,snp138,avsift \
    -operation g,g,f,f,f,f,f,f,f \
    -otherinfo \
    &>annovar.log

results in NPC.HK.12PY0019T-DNA.12PY0019.avinput and consequently NPC.HK.12PY0019T-DNA.12PY0019.hg19_multianno.vcf. Any idea why the -ensemble.temp3 is removed?

sxv commented 8 years ago

Figured it out! I was sending the wrong label via variable substitution.