Wildcards in regions bed file

[anuravi1234]

Hello,

I am trying to analyse RFC1 repeat expansions. The regions file provide the motif AAGGG howver RFC1 has several other motifs. I would like to know if it is possible to provide wildcards as (*) for the motif in the bed file. this will allow any RFC1 motifs to be detected.

I am using the Atarva version 0.6.0. I have already tried wildcards for RFC1 motifs and it doesnt not detect any motifs within RFC1. It will be nice to include this feature.

chr4 39348480 . aaaa . 0 PASS AC=0;AN=2;MOTIF=A*;START=39348479;END=39348483;ID=CANVAS_RFC1;REFCN=0 GT:AL:CN:AR:SD:DP:SN:SQ:MA:MR:DS:MV 0/0:4,4:0,0:4-79,4-79:30:30:.:.:.,.:.:.:.,.

[Dhaksnamoorthy]

Hi @anuravi1234,

Thanks for raising this issue and for using ATaRVa.

ATaRVa includes a built-in motif-decomposition feature that can identify and handle de novo motif variations within a repeat region. Therefore, it is not necessary to explicitly specify all possible motif variants in the BED file.

It also appears that the BED entry for RFC1 may be incorrect, as the region spans only 4 bp (39348479–39348483). We have uploaded the STRchive pathogenic loci BED file in the Catalogues folder; could you please try running ATaRVa using that BED file instead? I would also recommend updating to the latest release, ATaRVa v0.7.1.

We would be interested to know whether these changes resolve the issue. Your feedback would be very valuable in helping us improve ATaRVa further.

Thanks again!

[Dhaksnamoorthy]

Hi @anuravi1234,

Sorry, I missed your first question.

In the ATaRVa BED file format, wildcard characters (*) are not supported in the motif column. We recommend providing a single representative motif for each repeat region. For loci that can occur with multiple motif configurations (e.g., RFC1, BEAN1, and DAB1), we recommend specifying the motif with the max size or length as the representative motif in the BED file.

I hope this clarifies your doubt. Please let us know if you have any further questions.

[anuravi1234]

Dear @Dhaksnamoorthy

Sorry for my delayed reply and thank you for your reply to my queries. I have been using the bedfile from the Catalogues and also verified bedfile positions for RFC1. It is indeed 5 nucleotides from the start to the end position. I have also now upgraded Atarva to the 0.7.1 version.

Unfortunately I still get the same result. It seems like the motif length is only 2 nucleotides, even though it is mentioned as 5.

chr4 39348480 . aaaa AAAA 0 PASS AC=2;AN=2;MOTIF=AAAAG;START=39348479;END=39348483;ID=CANVAS_RFC1;REFCN=0 GT:AL:CN:LPM:AR:SD:DP:SN:SQ:MA:MR:DS:MV 1|1:4,4:0,0:AA-2,AA-2:4-4,2-4:8,6:20:1:24:.,.:.,.:(AA)2:.,.

This is how I run it

singularity exec \
        -B ${output}/${input}:/output \
        -B ${output}:/bed \
        -B ${files}/${input}:/input \
        -B ${path}/databases/UCSC_download:/ref \
        ${path}/my_tools/sifs/atarva_0_7_1.sif atarva genotype \
        -f /ref/human_selected_onlychr.fasta \
        -b /input/${input}_final.bam \
        -r /bed/STRchive-disease-loci.hg38.atarva.bed.gz \
        -o /output/${input}_atarva.vcf \
        --haplotag HP \
        --decompose \
        --loci-wise

It will be great if you can help me understand how to run this correctly.

Thank you!

[sowpati]

Dear @anuravi1234

Looking at your command, the BED file name still reflects the older file. Can you please confirm if you have downloaded the new BED file from the Catalogues, which was updated last week?

If you have used the updated BED file, then would it be possible for you to share any BAM file with us for debugging?

Cheers,
TEJ