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I perform variant calling on Amplicon Based Targeted Exome sequencing on Human.
I use a licenced version of GATK (V2014.3-3.2.2-7-g f9cba99).
I am using ReadBackedPhasing for obtaining the Phasing information.
After a successful run of the above tool, it displays that Sites phased are 41. (Screenshot attached)
However, in the output file I don't see any variant with a phased genotype.
The ReadBackedPhasing specific arguments provided are as given below:
java -jar ~/software_stack/GenomeAnalysisTK/GenomeAnalysisTK.jar -T ReadBackedPhasing -R ~/reference_stack/reference/human.fasta -I ~/dummydir/out.bam -V ~/dummydir/Sample.vcf -o ~/dummydir/Sample_Phased.vcf
I would also like to know what would be the ideal horizontal as well as vertical coverage (as per the interval file) for Amplicon based Targeted Exome sequencing to carry out a successful Genotype phasing.
Thanks & Regards,