how to get the phased vcf?

Hi there,

My container: pepper_deepvariant_test-v0.5.sif

My command:

run_pepper_margin_deepvariant call_variant \
        -b ${bam_file} \
        -f ${reference_file} \
        -t 16 \
        -o dv_out \
        --ont  \
        --phased_output​ \
        --gvcf

My output file list:

./logs
./logs/1_pepper_snp.log
./logs/2_margin_haplotag.log
./logs/3_pepper_hp.log
./logs/4_DeepVariant.log
./intermediate_files
./intermediate_files/PEPPER_HP_OUPUT.vcf.gz
./intermediate_files/PEPPER_HP_OUPUT.vcf.gz.tbi
./intermediate_files/PEPPER_SNP_OUPUT.vcf.gz
./intermediate_files/PEPPER_SNP_OUPUT.vcf.gz.tbi
./intermediate_files/MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam
./intermediate_files/MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam.bai
./intermediate_files/MARGIN_PHASED.PEPPER_SNP_MARGIN.chunks.csv
./PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz
./PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.g.vcf.gz
./PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.vcf.gz.tbi
./PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.g.vcf.gz.tbi
./PEPPER_MARGIN_DEEPVARIANT_FINAL_OUTPUT.visual_report.html

I’m looking around for errors in the logs but have only seen an error where deepvariant looks for CUDA, doesn’t find it, and defaults to the CPU analysis. Do you have any tips for how I can get the phased output?

[RichardCorbett]

I have been able to run 10 analyses successfully by making sure the .fai file is present with the .fa to keep margin from trying to create it. Don’t want to jinx it but this might be all I needed.

[RichardCorbett]

Thanks @kishwarshafin. I’ll let you know if anything changes on my end.