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Fixing Issue #32. We manually replaced the Number value from R to A for the NAF tag in the header of the DeepSomatic-outputted VCF #33

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Fixing Issue #32. We manually replaced the Number value from R to A for the NAF tag in the header of the DeepSomatic-outputted VCF #33

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17 changes: 17 additions & 0 deletions prep_vcfs_somatic/prep_vcf_somatic_functions.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,23 @@ function check_and_update_sample_names_for_deepsomatic(){
if [[ ${COUNT_NDP_TAG} -eq 1 && ${COUNT_NAD_TAG} -eq 1 && ${COUNT_NAF_TAG} -eq 1 && ${PRESENCE_TAG_NDP_IN_FORMAT} -eq 1 ]]
then
echo -e "\nFound that DeepSomatic has information about the Normal sample in the FORMAT field. Found NDP, NAD, NAF in Header and in NDP TAG FORMAT record of the first record" 1>&2
if [[ $(bcftools view -h --threads 3 ${VCF} | grep -c -m 1 "ID=NAF,Number=R") -eq 1 ]]
then
## a BUG in version DPS 1.10 exists; The NAF tag has been assigned Number=R instead of Number=A and that led to a bcftools failure.
## Here we update the VCF header to replace Number=R with Number=A for the NAF tag ; If we need to do it for other tags we will add more replacements here.
## Note: Number=A — One Value Per Alternate Allele ::::: example: VAF, only list the ALTernate Alleles frequency
## Note: Number=R — One Value Per Allele (Including Reference) ::: example: AD compared to VAF list the number of reads with the REFerence allele
## first we copy the VCF to make an intermediate name
rsync ${VCF} ${VCF}.tempFile
check_ev $? 'rsync deepsomatic v1.10 VCF'
## replacing header values
bcftools view --threads 3 ${VCF}.tempFile | sed 's/ID=NAF,Number=R/ID=NAF,Number=A/' | bcftools view --threads 3 -O z -o ${VCF} --write-index
check_ev $? 'update NAF numbering value R to A in VCF header'
# removing temp file has the original file has been overwritten
rm ${VCF}.tempFile 1>&2
## When Deepsomatic fixes that issue wew may remove the step above to speed thing up.
fi

VCF_NORMAL_TEMP=$( deepsomatic_make_normal_vcf_file_from_normal_tags_in_tumor_vcf ${VCF} ${TUMOR_SNAME} ${NORMAL_SNAME} )

else
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