yasin

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yasin
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Yasin Uzun

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  • The issue is, I only get a few variants as output, which does not seem realistic.
  • Here is the command I use: java -jar programs/gatk/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R genomes/hg19/ucsc.hg19.fasta \ -I input.ready.bam \ --dbsnp dbsnp/dbsnp_141.vcf \ -o variant_calling/haplo_depth/snps.g.vcf
  • I have a related question that I could not find the answer in here. I will appreciate of you can help. For the same individuals I mentioned above, I have RNA-Seq libraries in addition. May I take the advantage of those RNA-Seq libraries for variant…
  • Thank you. "...As long as the SM tags are identical, HaplotypeCaller will recognize that it's a single-sample run ..." This is the exact answer to my question.
  • Let me give the other details: INFO 11:47:28,551 HelpFormatter - Executing as... INFO 11:47:28,552 HelpFormatter - Date/Time: 2016/07/28 INFO 11:47:28,552 HelpFormatter - --------------------------------------------------------------------------…