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MNP detection using ReadBackedPhasing

GATK team,

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.


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