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Hi, I worked on CNSM VCF files downloaded from ICGC. I know the vcf files provided CN1 and CN2 values, but I notice a small amounts of mutations only have TCNexact values with CN1 and CN2. Such as below,
1 | 9509999 | . | N | . | PASS | END=9575012;STARTINT=[9509999,9510020];ENDINT=[9549973,9575012];CNVLEN=65014;TCNexact=1.13; | TCN:ACN | 1:./. | |
---|---|---|---|---|---|---|---|---|---|
1 | 72290017 | . | N | . | PASS | END=72319888;STARTINT=[72289966,72290068];ENDINT=[72319700,72320076];CNVLEN=29872;TCNexact=1.13; | TCN:ACN | 1:./. | |
1 | 72319888 | . | N | . | PASS | END=72383950;STARTINT=[72319700,72320076];ENDINT=[72383897,72383950];CNVLEN=64063;TCNexact=1.05; | TCN:ACN | 1:./. |
Do you know how to assign TCNexact value to CN1 and CN2?
Best wishes,
Lei
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