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center-for-computational-genomics-and-data-science
public
QuaC
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47ebad16
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47ebad16
authored
4 years ago
by
Manavalan Gajapathy
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adds column descriptions to multiqc template
parent
ef3b2744
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!2
QC under one umbrella (well mostly) under QuaC
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configs/multiqc_config_template.jinja2
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47 additions, 2 deletions
configs/multiqc_config_template.jinja2
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configs/multiqc_config_template.jinja2
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47ebad16
...
@@ -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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