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Commit 47ebad16 authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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adds column descriptions to multiqc template

parent ef3b2744
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1 merge request!2QC under one umbrella (well mostly) under QuaC
...@@ -251,32 +251,56 @@ custom_data: ...@@ -251,32 +251,56 @@ custom_data:
PCT_PF_READS_ALIGNED_val: PCT_PF_READS_ALIGNED_val:
min: {{ picard_asm_PCT_PF_READS_ALIGNED_min }} min: {{ picard_asm_PCT_PF_READS_ALIGNED_min }}
max: {{ picard_asm_PCT_PF_READS_ALIGNED_max }} max: {{ picard_asm_PCT_PF_READS_ALIGNED_max }}
description: "% of Pass filter(PF) reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS"
hidden: True hidden: True
PF_HQ_ALIGNED_Q20_BASES_val: PF_HQ_ALIGNED_Q20_BASES_val:
min: {{ picard_asm_PF_HQ_ALIGNED_Q20_BASES_min }} min: {{ picard_asm_PF_HQ_ALIGNED_Q20_BASES_min }}
description: "The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher."
hidden: True hidden: True
PCT_ADAPTER_val: PCT_ADAPTER_val:
min: {{ picard_asm_PCT_ADAPTER_min }} min: {{ picard_asm_PCT_ADAPTER_min }}
max: {{ picard_asm_PCT_ADAPTER_max }} max: {{ picard_asm_PCT_ADAPTER_max }}
description: "% of Pass filter(PF) reads that are unaligned and match to a known adapter sequence right from the start of the read."
hidden: True hidden: True
PCT_CHIMERAS_val: PCT_CHIMERAS_val:
min: {{ picard_asm_PCT_CHIMERAS_min }} min: {{ picard_asm_PCT_CHIMERAS_min }}
max: {{ picard_asm_PCT_CHIMERAS_max }} max: {{ picard_asm_PCT_CHIMERAS_max }}
description: "The number of chimeric pairs expressed as a % of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs."
hidden: True hidden: True
Q30_BASES_val: Q30_BASES_val:
min: {{ picard_qym_Q30_BASES_min }} min: {{ picard_qym_Q30_BASES_min }}
description: "The number of bases in all reads that achieve quality score 30 or higher"
hidden: True hidden: True
perc_Q30_BASES_val: perc_Q30_BASES_val:
min: {{ picard_qym_perc_Q30_BASES_min }} min: {{ picard_qym_perc_Q30_BASES_min }}
description: "% of bases in all reads that achieve quality score 30 or higher"
hidden: True hidden: True
PCT_EXC_TOTAL_val: PCT_EXC_TOTAL_val:
min: {{ picard_wgs_PCT_EXC_TOTAL_min }} min: {{ picard_wgs_PCT_EXC_TOTAL_min }}
max: {{ picard_wgs_PCT_EXC_TOTAL_max }} max: {{ picard_wgs_PCT_EXC_TOTAL_max }}
description: "% of aligned bases excluded due to all filters."
hidden: True hidden: True
PCT_15X_val: PCT_15X_val:
min: {{ picard_wgs_PCT_15X_min }} min: {{ picard_wgs_PCT_15X_min }}
max: {{ picard_wgs_PCT_15X_max }} max: {{ picard_wgs_PCT_15X_max }}
hidden: True description: "% of bases that attained at least 15X sequence coverage in post-filtering bases."
hidden: True
PCT_PF_READS_ALIGNED:
description: "% of Pass filter(PF) reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS"
PF_HQ_ALIGNED_Q20_BASES:
description: "The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher."
PCT_ADAPTER:
description: "% of Pass filter(PF) reads that are unaligned and match to a known adapter sequence right from the start of the read."
PCT_CHIMERAS:
description: "The number of chimeric pairs expressed as a % of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs."
Q30_BASES:
description: "The number of bases in all reads that achieve quality score 30 or higher"
perc_Q30_BASES:
description: "% of bases in all reads that achieve quality score 30 or higher"
PCT_EXC_TOTAL:
description: "% of aligned bases excluded due to all filters."
PCT_15X:
description: "% of bases that attained at least 15X sequence coverage in post-filtering bases."
qc_checkup_bcftools_stats: qc_checkup_bcftools_stats:
parent_id: "cgds_qc_checkup" parent_id: "cgds_qc_checkup"
...@@ -293,30 +317,51 @@ custom_data: ...@@ -293,30 +317,51 @@ custom_data:
number_of_records_val: number_of_records_val:
min: {{ bcftools_stats_number_of_records_min }} min: {{ bcftools_stats_number_of_records_min }}
max: {{ bcftools_stats_number_of_records_max }} max: {{ bcftools_stats_number_of_records_max }}
description: "Number of variants"
hidden: True hidden: True
number_of_SNPs_val: number_of_SNPs_val:
min: {{ bcftools_stats_number_of_SNPs_min }} min: {{ bcftools_stats_number_of_SNPs_min }}
max: {{ bcftools_stats_number_of_SNPs_max }} max: {{ bcftools_stats_number_of_SNPs_max }}
description: "Number of SNPs"
hidden: True hidden: True
number_of_indels_val: number_of_indels_val:
min: {{ bcftools_stats_number_of_indels_min }} min: {{ bcftools_stats_number_of_indels_min }}
max: {{ bcftools_stats_number_of_indels_max }} max: {{ bcftools_stats_number_of_indels_max }}
description: "Number of Insertions/Deletions"
hidden: True hidden: True
perc_snps_val: perc_snps_val:
min: {{ bcftools_stats_perc_snps_min }} min: {{ bcftools_stats_perc_snps_min }}
max: {{ bcftools_stats_perc_snps_max }} max: {{ bcftools_stats_perc_snps_max }}
description: "% SNPs"
hidden: True hidden: True
perc_indels_val: perc_indels_val:
min: {{ bcftools_stats_perc_indels_min }} min: {{ bcftools_stats_perc_indels_min }}
max: {{ bcftools_stats_perc_indels_max }} max: {{ bcftools_stats_perc_indels_max }}
description: "% Insertions/Deletions"
hidden: True hidden: True
tstv_val: tstv_val:
min: {{ bcftools_stats_tstv_min }} min: {{ bcftools_stats_tstv_min }}
max: {{ bcftools_stats_tstv_max }} max: {{ bcftools_stats_tstv_max }}
description: "SNPs transition / transversion ratio"
hidden: True hidden: True
heterozygosity_ratio_val: heterozygosity_ratio_val:
min: {{ bcftools_stats_heterozygosity_ratio_min }} min: {{ bcftools_stats_heterozygosity_ratio_min }}
hidden: True description: "No. of het sites in an individual divided by the no. of non-reference hom sites. Note: This varies heavily across populations."
hidden: True
number_of_records:
description: "Number of variants"
number_of_SNPs:
description: "Number of SNPs"
number_of_indels:
description: "Number of Insertions/Deletions"
perc_snps:
description: "% SNPs"
perc_indels:
description: "% Insertions/Deletions"
tstv:
description: "SNPs transition / transversion ratio"
heterozygosity_ratio:
description: "No. of het sites in an individual divided by the no. of non-reference hom sites. Note: This varies heavily across populations."
qc_checkup_variant_per_contig: qc_checkup_variant_per_contig:
parent_id: "cgds_qc_checkup" parent_id: "cgds_qc_checkup"
......
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