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RB_74

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RB_74
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  • Hi have question in the same line... For filter snp and indels and i have used following filter --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 20.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' \ --filterNam…
  • @Geraldine_VdAuwera when i am running java -jar GenomeAnalysisTK.jar -R mm10_genome.fa -T VariantsToVCF -V:OLDDBSNP snp142.txt -o dbsnp142.vcf I am getting the following error: ERROR MESSAGE: Invalid command line: No tribble type was provide…
  • Hi Sheila, I encountered same problem. I have many like with first warning and few with second one. ${JAVA} -jar ${BIN_PATH}/GenomeAnalysisTK.jar -T VariantFiltration -R ${GENOME_FILE} -V ${RAWSNPS_OUTPUT} --filterExpression 'QD < 2.0 || F…
  • Hi Sheila, Thank you for the article. This will greatly solve my problem. And I ran the command java -jar ../bin/GenomeAnalysisTK.jar -T HaplotypeCaller -R ${GENOME_FILE} -I S1_recal_reads.bam -o S1_merge_recal_snps.vcf -bamout S1_recal_reads.b…
  • Hi EADG, Thank you for this. If I understood it correctly from the link I should use these new Bam file to view the SNPs. I am running to test this for one sample with the command below java -jar ../bin/GenomeAnalysisTK.jar -T HaplotypeCaller…