I used Haplotypecaller 3.1 to detect MNP variants. java -Xmx6g -Djava.io.tmpdir=$PWD -jar $GATK -R $hg19 -T HaplotypeCaller -I $bamlist --dbsnp $dpsnp135 -o $call/$sample.all.vcf -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 200 -nct $nct -A SpanningDeletions -A TandemRepeatAnnotator -A HomopolymerRun -A AlleleBalance -l INFO -baqGOP 30 --max_alternate_alleles 2 -rf BadCigar --minPruning 5
The result had no MNP type varaints, but I can find some continuous snp variants. these snp variants didn't be combined to MNP variants. Is this normal ? or I really didn't get MNP variants ?