Illumina tumor samples without normal

[gl00ten]

I have Illumina tumor samples without normal <- for this case which flag should I use?

[
    'WGS',
    'WES',
    'PACBIO',
    'ONT',
    'FFPE_WGS',
    'FFPE_WES',
    'WGS_TUMOR_ONLY',
    'PACBIO_TUMOR_ONLY',
    'ONT_TUMOR_ONLY',
],

None seems appropriate at first glance.

edit: I have WES samples, not WGS

[pichuan]

Hi @gl00ten , please use WGS_TUMOR_ONLY

[gl00ten]

@pichuan sorry I forgot to mention I have WES not WGS. Which do I use?

[pichuan]

Hi @gl00ten ,
Please use WGS_TUMOR_ONLY for Illumina WES data as well.

Thank you!

[gl00ten]

Hi again @pichuan

I'm getting a bunch of these errors as I start to run deepsomatic

population_vcf does not have config NC_000001.11

running like so:

INPUT_DIR="${PWD}/mydata"
BIN_VERSION="1.8.0"

OUTPUT_DIR="${PWD}/quickstart-output"
mkdir -p "${OUTPUT_DIR}"

sudo docker run \
-v ${INPUT_DIR}:${INPUT_DIR} \
-v ${OUTPUT_DIR}:${OUTPUT_DIR} \
google/deepsomatic:"${BIN_VERSION}" \
run_deepsomatic \
--model_type=WGS_TUMOR_ONLY \
--ref=${INPUT_DIR}/genomes/human_GRCh38.p14/GRCh38_latest_genomic.fna \
--reads_tumor=${INPUT_DIR}/101B.bam \
--output_vcf=${OUTPUT_DIR}/101B_WGS_TUMOR_ONLY.vcf.gz \
--output_gvcf=${OUTPUT_DIR}/101B_WGS_TUMOR_ONLY.g.vcf.gz \
--sample_name_tumor="tumor" \
--num_shards=28 \
--logging_dir=${OUTPUT_DIR}/logs \
--vcf_stats_report=true \
--intermediate_results_dir ${OUTPUT_DIR}/intermediate_results_dir \

Did I use the wrong reference format ?

Want me to open a new ticket for this?

[pichuan]

Hi @gl00ten , can you try specifying the contig(s) that you want to call, and first confirm if that works or not?

For example, add a flag --regions=chr1 first to confirm that works or not.