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3.0 years ago
michael.flower.14
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200
I'm dealing with paired end amplicon sequencing data. I've produced a GVCF file with haplotype calls using:
gatk HaplotypeCaller -R $REF -I "$BAM" -O "$OUT"/results/variants/${SN}_HaplotypeCallerPGT.vcf -ERC GVCF
The vcf file it produces contains the PGT flag, and variants are called in the format 0|1.
I'm then calling the consensus sequence for each haplotype using
samtools faidx "$REF" chr5:80654720-80655181 | bcftools consensus -p "$PREFIX" -H 1pIu "$PREFIX".vcf.gz > "$OUT"/results/consensus/${SN}_consensus.1pIu.fa
samtools faidx "$REF" chr5:80654720-80655181 | bcftools consensus -p "$PREFIX" -H 2pIu "$PREFIX".vcf.gz > "$OUT"/results/consensus/${SN}_consensus.2pIu.fa
But the sequence of both 1plu and 2plu files is exactly the same. Surely variants should segregate as per the PGT flag??
