Sann

Hi Dan, I have got something different problem. I assume this is a problem with Varscan. I am using varscan to call variants that meet desired thresholds using the command java -jar VarScan.v2.3.9.jar mpileup2cns mydata.mpileup --min-coverage 10 --min-var-freq 0.90 --p-value 0.005 --variants > variants_varscan.vcf After Varscan i am running snpEff to annotate the variants but the snpEff output shows SNP=0, INS=48 and MIXED=6 . The snpEff command: java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_000277735...

Hi, I assume this is a problem with Varscan. I am using varscan to call variants that meet desired thresholds using the command java -jar VarScan.v2.3.9.jar mpileup2cns mydata.mpileup --min-coverage 10 --min-var-freq 0.90 --p-value 0.005 --variants > variants_varscan.vcf After Varscan i am running snpEff to annotate the variants but the snpEff output shows SNP=0, INS=48 and MIXED=6 . The snpEff command: java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_000277735 variants_varscan.vcf...

Hi, I am pretty new in this environment. I wonder if there is a Mycobacterium tuberculosis reference genome in snpeff database that can be used to annotate variants in .vcf format. I have downloaded recent version from here: http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip