Closed lk9-lnx closed 2 years ago
/opt/VarDictJava/VarDict/vardict -G genome.fa -q 15 -f 0.01 -N case -b case.bam -c 1 -S 2 -E 3 -g 4 bed_file.bed > case.vcf
/opt/VarDictJava/VarDict/vardict -G genome.fa -th -q 15 -f 0.01 -N case -b case.bam -c 1 -S 2 -E 3 -g 4 bed_file.bed > case.vcf
Why i am seeing a variant with -th option in the vcf option that I don't see without providing the option? what does -th do? The vcf file has lot more variants with -th option.
not called
/opt/VarDictJava/VarDict/vardict -G genome.fa -q 15 -f 0.01 -N case -b case.bam -c 1 -S 2 -E 3 -g 4 bed_file.bed > case.vcf
called
/opt/VarDictJava/VarDict/vardict -G genome.fa -th -q 15 -f 0.01 -N case -b case.bam -c 1 -S 2 -E 3 -g 4 bed_file.bed > case.vcf
Why i am seeing a variant with -th option in the vcf option that I don't see without providing the option? what does -th do? The vcf file has lot more variants with -th option.