The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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.