Generate multiqc report only

[vatanparast]

Hello,

Is there any way to run pggb to generate multiqc report without running entire analyses?

In the current multiqc report, the "Variant Quality" report is empty. I am not sure why?

Bcftools version is 1.19; pggb is v0.7.2; MultiQC v1.22.2

Many thanks,

[subwaystation]

Hi @vatanparast. Yes, this is possible in principle. Take a look at the line

pggb/pggb

Line 915 in fb25f87

if [[ $multiqc == true ]]; then

and following. You can generate the MultiQC config as shown in https://github.com/pangenome/pggb/blob/fb25f8731ab10a2beb35f0855faad229fac5e3eb/pggb#L853-913 or copy it from https://github.com/nf-core/pangenome/blob/master/assets/multiqc_config.yml.

Regarding your first question: I would guess you didn't run vg deconstruct?

[subwaystation]

Ah no you have INDELs. Good question. I assume it is an issue with the bcftools module in MultiQC. Else I currently don't have any ideas.

[subwaystation]

You have SNPs in your VCF?

[vatanparast]

Hi @subwaystation

I would guess you didn't run vg deconstruct?

No, I haven't run it. Should I run it after the PGGB job?

You have SNPs in your VCF?

Yes, there are SNPs in the VCF file. Please see below from the .decomposed.vcf.

##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##INFO=<ID=CONFLICT,Number=.,Type=String,Description="Sample names for which there are multiple paths in the graph with conflicting alleles"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=LV,Number=1,Type=Integer,Description="Level in the snarl tree (0=top level)"> ##INFO=<ID=PS,Number=1,Type=String,Description="ID of variant corresponding to parent snarl"> ##INFO=<ID=AT,Number=R,Type=String,Description="Allele Traversal as path in graph"> ##contig=<ID=Cantata#1#Scf9YQZ_11_HRSCAF_22,length=53816809> ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> ##INFO=<ID=ORIGIN,Number=1,Type=String,Description="Decomposed from a complex record using vcflib vcfwave and alignment with WFA2-lib."> ##INFO=<ID=INV,Number=0,Type=Flag,Description="Inversion detected"> ##bcftools_annotateVersion=1.19+htslib-1.19 ##bcftools_annotateCommand=annotate -x INFO/TYPE; Date=Thu Nov 14 08:35:25 2024 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FRAX_001_PL PG5 Cantata#1#Scf9YQZ_11_HRSCAF_22 2759 >5>8 A C 60 . AC=1;AF=1;AN=1;AT=>5>6>8,>5>7>8;NS=1;LV=0 GT . .|1 Cantata#1#Scf9YQZ_11_HRSCAF_22 2761 >8>11 A G 60 . AC=1;AF=1;AN=1;AT=>8>9>11,>8>10>11;NS=1;LV=0 GT . .|1 Cantata#1#Scf9YQZ_11_HRSCAF_22 2834 >11>14 A G 60 . AC=1;AF=1;AN=1;AT=>11>12>14,>11>13>14;NS=1;LV=0 GT . .|1 Cantata#1#Scf9YQZ_11_HRSCAF_22 2852 >14>16 G GT 60 . AC=1;AF=1;AN=1;AT=>14>16,>14>15>16;NS=1;LV=0 GT . .|1

[subwaystation]

No, I haven't run it. Should I run it after the PGGB job?

You already produced a VCF, so you should be good.

Yes, there are SNPs in the VCF file. Please see below from the .decomposed.vcf.

Hmm... can you share all produced VCF? If too large here send a mail to [email protected]

[huw143]

In my report, I also have same issue here. Jus leave a mark here