Scope and Principles of Long-Read QC Metrics - Variant level

[justinjj24]

Metrics:: Variant-level

• SNVs count

• Indels count (short indels | long indels) – Insertion and Deletion
  Scope and Principles for Long-Read QC Standard Metrics - Indels #116

• Insertions / Deletions ratio

• Heterozygous / Homozygous ratio (SNVs | Indels)

• Transition / Transversion (Ti/Tv) rate

• Phase block NG50

[justinjj24]

NG50 phase block based metrics were agreed to be valuable; however, in the absence of a phased VCF, no values (Nil) should be reported. These metrics will be considered optional/advanced and reported only when phased VCFs are available?

Phase block NG50 metric measure the length of phased variant blocks across the genome, not the reads. These blocks are defined relative to a reference genome length, which is why NG50 is the standard metric. Because this stage is independent of how the reads were generated, the same NG50 definition applies to PacBio, ONT, and Constellation.

[justinjj24]

Indels:: Insertions and Deletions The QC framework is fundamentally downstream of BAM/CRAM and VCF. V2 will focus on VCF-based indels only, even if they are larger in size due to long reads. These indels are treated as “Large indels enabled by long-read sequencing” Not as fully defined structural variants. Treat large long-read indels as an extension of indel QC, Not as full structural variants.
Not explicitly treat Short-indel (ABS(LEN) <50)? OR
bcftools view -H -v indels -f PASS -i {‘ILEN>0’} -R %s %s | wc -l" % (regions, input_vcf)
bcftools view -H -v indels -f PASS -i {‘ILEN<0’} -R %s %s | wc -l" % (regions, input_vcf)