Haplotype caller

sridhar28sridhar28 Posts: 13Member
edited July 2013 in Ask the GATK team

Dear Team,
i am using Haplotype caller to identify the indels in my sequence..
i am running it in command line..

java -jar /illumina/data/galaxy/apps/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T HaplotypeCaller -R genome.fa -I S21_full.picard.bam -o indels_S21.vcf

but i couldnt find any entries in the output file, also the file size shows 0..

INFO 09:14:25,280 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining

INFO 09:14:55,283 ProgressMeter - chr1:4710472 4.72e+06 30.0 s 6.0 s 0.2% 5.5 h 5.4 h

INFO 09:15:25,284 ProgressMeter - chr1:8280981 8.29e+06 60.0 s 7.0 s 0.3% 6.2 h 6.2 h

INFO 09:15:55,285 ProgressMeter - chr1:11311033 1.13e+07 90.0 s 7.0 s 0.4% 6.8 h 6.8 h

INFO 09:16:25,286 ProgressMeter - chr1:15877953 1.59e+07 120.0 s 7.0 s 0.5% 6.5 h 6.5 h

INFO 09:16:55,287 ProgressMeter - chr1:19156923 1.92e+07 2.5 m 7.0 s 0.6% 6.7 h 6.7 h

INFO 09:17:25,288 ProgressMeter - chr1:22167191 2.22e+07 3.0 m 8.0 s 0.7% 7.0 h 6.9 h

INFO 09:17:55,289 ProgressMeter - chr1:24574489 2.46e+07 3.5 m 8.0 s 0.8% 7.3 h 7.3 h

Please suggest on the same..

Thanks
Sridhar

Post edited by sridhar28 on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Hi there,

    It looks like when you posted this, your job was still running, or did you truncate the output?

    Geraldine Van der Auwera, PhD

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