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  • HII luca beltrame Can you please let me know from where and how to install gsalib. Because i also have run Base-recalibration step that is creating plot .grp file but not creating plot pdf file. Please let me know how to generate plot pdf file Tha…
  • I have seen complete thread, i have Installed Rscript, ggplot2 . commnd is working fine , not giving any eror and creating recal.grp file also but noty creating plot pdf. after running commnd few lines are like this INFO 18:58:46,524 BaseRecalibr…
  • I am running BaseRecalibrator command its running for IONTORRENT data , creating recal.grp file but not creating any plot pdf. I have seen all comments given in mailing list…
  • My reference gene is of 1400 NT long and i have given the coordinate -L 22:52564000-52565300, Its giving error Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The genome loc coordinates 52564000-52565300 exceed the contig size (…
  • Thanks i used java -Xmx2g -jar GenomeAnalysisTK.jar -T SelectVariants -R CATHL1.fasta --variant Bostaurus.vcf -o newbos.vcf -L chr22:52561651-52566504, still getting error Badly formed genome loc: Contig 'chr22' does not match any contig in the GA…
  • Thanks 1- I started First step u told me, Now Please let me know how to define coordinates in SelectVariants Command , as the position of my CATHL1 gene in Genome is chr22:52,563,935-52,565,359. and what is -L argument ? I used java -Xmx2g -jar Gen…
  • Hii Cecmonat I am also getting the same memory problem.I tried with -Xmx4g, -Xmx16g still no solution please let me know how to solve that. Thanks
  • Thanks Geraldine Means i can do Ion torrent analysis using Gatk. My second query is that like RGPL is Read group Platform so what does it means of RGLB, RGSM and RGPU mentioned in gatk tutorial Mapping and duplicate marking Thanks