MNP detection using ReadBackedPhasing
I have used HaplotypeCaller to call variations in the exome data, performing joint calling on the samples. Then, ReadBackedPhasing was running on each sample individually with "-enableMergeToMNP" option. I was expecting to get the phased SNPs merged into MNPs. In the attached screenshot of one of the samples, I expect TG>CA, since I have not changed the default option of -maxDistMNP. This is the screen shot of phased VCF file output from ReadBackedPhasing.
19 1037715 rs200177867 T C 68058.90 PASS . GT:AD:DP:GQ:HP:PGT:PID:PL 0/1:23,7:30:99:1037715-1,1037715-2:0|1:1037715_T_C:198,0,1019 19 1037716 rs201532581 G A 68349.90 PASS . GT:AD:DP:GQ:HP:PGT:PID:PL:PQ 0/1:24,6:30:99:1037715-1,1037715-2:0|1:1037715_T_C:198,0,1019:1092.06 19 1037718 rs199741851 G T 67457.30 PASS . GT:AD:DP:GQ:HP:PGT:PID:PL:PQ 0/1:24,6:30:99:1037715-1,1037715-2:0|1:1037715_T_C:177,0,1022:1100.75
Command used :
java -jar GATK \ -T ReadBackedPhasing \ -R EnsemblhgGRCh37_71.karyoorder.gatk.fa \ -I file.bam \ --variant f.recode.vcf \ -o phased_f.vcf \ -enableMergeToMNP \ --phaseQualityThresh 20.0
Please let me know if the command needs additional parameters. Thanks.