Bundle lineage-references and outgroup

[abhi18av]

Based on some recent uses of the pipeline, it was necessary to have some strains from different lineages as well as an outgroup.

I was wondering whether we should add a database similar to EXIT-RIF so that people can just turn on that option.

We've had some conversation over emails regarding this, boiling down to

1. Using -k 66 with BWA_MEM since older
2. Reducing the 4 quality thresholds to push through majority of samples

[abhi18av]

Following up on the previous discussions (please feel free to add your thoughts here)

1. I used the GVCFs generated by the CALL_WF GATK Haplotype process and created a minimal GVCF for LineageAndOutgroup as well as LineageAndOutgroupAndEXITRIF.

gatk CombineGVCFs --java-options "-Xmx4G" \
    -R NC-000962-3-H37Rv.fa \
     -G StandardAnnotation -G AS_StandardAnnotation  \
    --variant MTb_L9.ERR4162024.g.vcf.gz  --variant MTb_L1.SAMN10185847.g.vcf.gz  --variant MTb_L7.ERR1971849.g.vcf.gz  --variant MTb_L6.SAMEA1877150.g.vcf.gz  --variant MTb_L8.SRR10828835.g.vcf.gz  --variant MTb_L410.ERR216945.g.vcf.gz  --variant MTb_L5.SAMEA1877169.g.vcf.gz  --variant MTb_L2.SAMEA1877219.g.vcf.gz  --variant MTb_L43.ERR1193883.g.vcf.gz  --variant MTb_L3.SAMEA1877181.g.vcf.gz  \
    --variant Mcanettii.ERR5104570.g.vcf.gz \
    --variant EXIT-RIF.g.vcf.gz  \
    -O LineagesAndOutgroupsAndEXITRIF.g.vcf.gz

2. Then fed the GVCF file instead of any FASTQ, therefore they were incorporated in the MERGE_WF directly by skipping the filtration processes.

use_ref_exit_rif_gvcf: true

ref_exit_rif_gvcf: /MAGMA_MTB_PROJECTS/data/exit-rif/LineagesAndOutgroups.g.vcf.gz

ref_exit_rif_gvcf_tbi: /MAGMA_MTB_PROJECTS/data/exit-rif/LineagesAndOutgroups.g.vcf.gz.tbi

UPDATE (08-AUG-2023): Tim confirmed that using this GVCF the phylogeny looks spot-on https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000477

[abhi18av]

Temporary location and permanent MD5 sums of the files documented above

https://transfer.sh/AHUxP8LoVa/LineagesAndOutgroups.g.vcf.gz
https://transfer.sh/hul8Y16tyV/LineagesAndOutgroups.g.vcf.gz.tbi

And here are the MD5 sums

767eeb74076df4edfa6188e9af8e6a98  LineagesAndOutgroups.g.vcf.gz
ba260ee60652e5a04918bbba7bf02082  LineagesAndOutgroups.g.vcf.gz.tbi