Count covariates ERROR

Question

[cristina_sabiers]

WELL..IM GOING TO DIE XD

This pipeline should really need to be updated.

http://seqanswers.com/wiki/How-to/exome_analysis

Im now at step, Quality score recalibration , This step didnt work for me

1) Count covariates:

java -Xmx4g -jar /home/cri/Desktop/GATK/GenomeAnalysisTK.jar \
-l INFO \
-R hg19.fa \
--DBSNP dbsnp132.txt \
-I input.header.realigned.bam \
-T CountCovariates \
-cov ReadGroupCovariate \
-cov QualityScoreCovariate \
-cov CycleCovariate \
-cov DinucCovariate \
-recalFile input.recal_data.csv

so instead I used this one

 java -jar /home/cri/Desktop/GATK/GenomeAnalysisTK.jar \
   -T BaseRecalibrator \
   -R hg19.fa \
   -I input.header.realigned.bam \
   -knownSites /media/cri/CRIS_DATA/All_20160407.vcf \
   -o recal_data.table

wget -c ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/GATK/All_20160407.vcf.gz

sadly got a new ERROR...

ERROR MESSAGE: The platform (Ion Torrent) associated with read group GATKSAMReadGroupRecord @RG:1 is not a recognized platform. Allowable options are ILLUMINA,SLX,SOLEXA,SOLID,454,LS454,COMPLETE,PACBIO,IONTORRENT,CAPILLARY,HELICOS,UNKNOWN

samtools view -H input.header.realigned.bam | grep '^@RG'
@RG ID:1    PU:RUN  LB:LIBRARY  SM:SAMPLE   CN:BCM  PL:Ion Torrent

Is because PL is Ion Torrent instead IONTORRENT?

Any suggestion how I can fix this issue?

Thanks

Answer 1

[russhh]

The given error message would go away if you use IONTORRENT. Whether any further errors will crop up, I'm unsure...

[cristina_sabiers]

Thanks Russhh, I changed PL for IONTORRENT...Is working now :)