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google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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Why all the GT of the PASS variant site is 1/1? use deepsomatic #848

Closed DayTimeMouse closed 2 months ago

DayTimeMouse commented 2 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 2 months ago

Hi @DayTimeMouse Please see https://github.com/google/deepsomatic/issues/16#issuecomment-2214935507 , which points to https://github.com/google/deepsomatic/issues/3

I kept your other question on DeepSomatic open: https://github.com/google/deepsomatic/issues/17 (which I also gave the same answer above. So I'll close this issue.