Functions

count_deletions(mqc, biosample_id)	Description: The ratio between number of insertion and deletion in VCF, only in autosomal regions, high quality variants.
count_insertions(mqc, biosample_id)	Description: The number of variant type indels only insertions in VCF, only in autosomal regions, high quality variants.
count_snvs(mqc, biosample_id)	Description: The number of variant type SNVs in VCF, only in autosomal regions, high quality variants.
cross_contamination_rate(mqc, biosample_id)	Description: Estimation of inter-sample contamination rate of short paired-end sequencing high quality, non duplicated reads, primary alignments, mapped on GRCh38 assembly.
insert_size_std_deviation(mqc, biosample_id)	Description: The insert size standard deviation of short paired-end sequencing high quality reads, primary alignments, mapped on GRCh38 assembly.
mad_autosome_coverage(mqc, biosample_id)	Description: The median absolute deviation of sequencing coverage derived from short paired-end sequencing high quality, non duplicated reads, primary alignments, achieving a base quality of 20 or greater and mapping quality of 20 or greater, in autosomes non gap regions of GRCh38 assembly.
mean_autosome_coverage(mqc, biosample_id)	Description: The mean sequencing coverage derived from short paired-end sequencing high quality, non duplicated reads, primary alignments, achieving a base quality of 20 or greater and mapping quality of 20 or greater, in autosomes non gap regions of GRCh38 assembly.
mean_insert_size(mqc, biosample_id)	Description: The mean insert size of short paired-end sequencing high quality reads, primary alignments, mapped on GRCh38 assembly.
pct_autosomes_15x(mqc, biosample_id)	Description: The percentage of bases attaining at least 15X sequencing coverage in short paired-end sequencing high quality, non duplicated reads, primary alignments, achieving a base quality of 20 or greater and mapping quality of 20 or greater, in autosomes non gap regions of GRCh38 assembly.
pct_reads_mapped(mqc, biosample_id)	Description: The percentage of short paired-end sequencing high quality reads, primary alignments, mapped on GRCh38 assembly.
pct_reads_properly_paired(mqc, biosample_id)	Description: The percentage of short paired-end sequencing high quality, properly paired reads, primary alignments, mapped on GRCh38 assembly.
ratio_heterozygous_homzygous_indel(mqc, ...)	Description: The ratio of heterozygous and homozygous variant type indels in VCF, only in autosomal regions, high quality variants.
ratio_heterozygous_homzygous_snv(mqc, ...)	Description: The ratio of heterozygous and homozygous variant type SNVs in VCF, only in autosomal regions, high quality variants.
ratio_insertion_deletion(mqc, biosample_id)	Description: The ratio between number of insertion and deletion in VCF, only in autosomal regions, high quality variants.
ratio_transitions_transversions(mqc, ...)	Description: The ratio of transitions and transversions of bi-allelic SNVs in VCF, only in autosomal regions, high quality variants.
yield_bp_q30(mqc, biosample_id)	Description: The number of bases in short paired-end sequencing high quality reads, primary alignments, achieving a base quality score of 30 or greater (Phred scale).