Add phasing to SNV VCF

[geocarvalho]

docker run -v $PWD:$PWD biocontainers/bcftools:v1.9-1-deb_cv1 bcftools view -i 'GT="0/0" || GT="0/1" || GT="1/1"' $PWD/MGD9213-P_blood_wgs.deepvariant.vcf > $PWD/MGD9213-P.diploid.vcf

docker pull quay.io/biocontainers/hapcut2:1.3.4--h7e4f606_2
docker run -v $PWD:$PWD quay.io/biocontainers/hapcut2:1.3.4--h7e4f606_2 /usr/local/bin/extractHAIRS --ref $PWD/ucsc/bwamem2/hg38.fa --bam $PWD/UDN/MGD9213-P_blood_wgs.cram --VCF $PWD/UDN/MGD9213-P.diploid.vcf --out $PWD/UDN/fragment_file

docker run -v $PWD:$PWD quay.io/biocontainers/hapcut2:1.3.4--h7e4f606_2 /usr/local/bin/HAPCUT2 --fragments $PWD/fragment_file --VCF $PWD/UDN367823-P.vcf --output $PWD/UDN367823-P.haplotype_output_file

[geocarvalho]

# whatshap
docker run -v $PWD:$PWD biocontainers/bcftools:v1.9-1-deb_cv1 bcftools merge -O z $PWD/MGD9213-P_blood_wgs.deepvariant.vcf.gz $PWD/MGD9216-M_blood_wgs.deepvariant.vcf.gz > $PWD/MGD9213-P_MGD9216-M.joint.vcf.gz

docker run -v $PWD:$PWD quay.io/biocontainers/samtools:1.22.1--h96c455f_0 samtools view -H $PWD/MGD9213-P_blood_wgs.cram | grep SM
@RG     ID:MGD9213-P_blood_wgs  CN:CN   LB:MGD9213-P_blood_wgs  PL:ILLUMINA     PU:MGD9213-P_blood_wgs  SM:MGD9213-P_blood_wgs

docker run -v $PWD:$PWD quay.io/biocontainers/samtools:1.22.1--h96c455f_0 samtools view -H $PWD/MGD9216-M_blood_wgs.cram | grep SM
@RG     ID:MGD9216-M_blood_wgs  CN:CN   LB:MGD9216-M_blood_wgs  PL:ILLUMINA     PU:MGD9216-M_blood_wgs  SM:MGD9216-M_blood_wgs

vim MGD9213-P_cohort.ped
FAM1  MGD9213-P_blood_wgs    0   MGD9216-M_blood_wgs   2   -9
FAM1  MGD9216-M_blood_wgs   0   0   2   -9

docker run -v $PWD:$PWD quay.io/biocontainers/whatshap:2.8--py312hf731ba3_0 whatshap phase \
    --ped $PWD/UDN/MGD9213-P_cohort.ped \
    -o $PWD/UDN/MGD9213-P_MGD9216-M_phased.vcf.gz \
    --reference $PWD/ucsc/bwamem2/hg38.fa \
    $PWD/UDN/MGD9213-P_MGD9216-M.joint.vcf.gz \
    $PWD/UDN/MGD9213-P_blood_wgs.cram \
    $PWD/UDN/MGD9216-M_blood_wgs.cram