search

ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
49 stars 25 forks source link

BCF: incorrect number of fields (6 != 5) at 927143687:4074044 #260

Closed zhangjianruwang closed 6 years ago

zhangjianruwang commented 6 years ago 
      the command I use to produce BCF is

samtools mpileup -gDf hg19 female.bam male.bam offspring.bam

      the colume title of BCF is

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT female male offspring

      the command I use to call denovo mutations is

dng dnm auto --ped ped --bcf bcf 

      and I got this error in two trios

incorrect number of fields (6 != 5) at *:

zhangjianruwang commented 6 years ago

So what the error is? how can I solve it?

jgarciamesa commented 6 years ago

What version of bfctools are you using? (bcftools --version) Also, what version of DeNovoGear are you using?

reedacartwright commented 6 years ago

The error occurs when you use a recent version of bcftools with an old version of dng dnm. Try installing from the develop branch.

-- Reed A. Cartwright, PhD Barrett Honors Faculty Assistant Professor of Genomics, Evolution, and Bioinformatics School of Life Sciences Human and Comparative Genomics Laboratory The Biodesign Institute Arizona State University

Availability: http://links.asu.edu/CartwrightCalendar Address: The Biodesign Institute, PO Box 875301, Tempe, AZ 85287-5301 USA Packages: The Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ 85287-5301 USA Office: Biodesign B-220C, 1-480-965-9949 Website: http://cartwrig.ht/

On Wed, Apr 4, 2018 at 12:15 PM, Juan J. Garcia Mesa < notifications@github.com> wrote:

What version of bfctools are you using? (bcftools --version) Also, what version of DeNovoGear are you using?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/denovogear/denovogear/issues/260#issuecomment-378714008, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGOHmkJOBc6_SavPftmFft-ANQQaSbYks5tlRvdgaJpZM4TGg1A .

reedacartwright commented 6 years ago

Marking: Resolved in Develop branch.