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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
BSD 3-Clause "New" or "Revised" License
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Why all the GT of the PASS variant site is 1/1? #17

Closed DayTimeMouse closed 4 months ago

DayTimeMouse commented 4 months ago

Hi,

Why all the GT of the PASS variant site is 1/1? use deepsomatic.

chr1 91748 . C T 10 PASS . GT:GQ:DP:AD:VAF:PL 1/1:10:61:48,13:0.213115:9,19,0

The command:

BIN_VERSION="1.6.1" docker run -v "${INPUT_DIR}":"/input" -v "${OUTPUT_DIR}:/output" google/deepsomatic:"${BIN_VERSION}" run_deepsomatic --model_type=PACBIO --ref=/input/chm13v2.0.fa --reads_normal=/input/hifi_normal.bam --reads_tumor=/input/hifi_tumor.bam --output_vcf=/output/somatic_output_vcf.gz --output_gvcf=/output/somatic_output_g.vcf.gz --sample_name_tumor="tumor" --sample_name_normal="normal" --num_shards=48 --logging_dir=/output/logs --intermediate_results_dir=/output/intermediate_results_dir

Best wishes.

pichuan commented 4 months ago

Hi @DayTimeMouse , can you take a look at my answer in https://github.com/google/deepsomatic/issues/16#issuecomment-2214935507 ?

I'll keep this open for now.