Null iterator

[asylvz]

Hello,

Is there any specific alignment commands I should use to create the BAM file? I used "minimap2 -cx map-ont", and the command "vamos-v1.2.0_x64-linux --contig -b NA19129_H1_grch38.bam -r vntr_region_motifs.o.bed.gz -s NA19129 -o NA19129.hap1.vcf -t 8"

However I get a lot of "[E::sam_itr_next] Null iterator" lines and the final VCF has only the header lines.

Thank you, Arda

[mchaisso]

Can you run on an unzipped version of the bed file?

On Mon, Jun 3, 2024 at 4:51 AM Arda Söylev @.***> wrote:

Hello,

Is there any specific alignment commands I should use to create the BAM file? I used "minimap2 -cx map-ont", and the command "vamos-v1.2.0_x64-linux --contig -b NA19129_H1_grch38.bam -r vntr_region_motifs.o.bed.gz -s NA19129 -o NA19129.hap1.vcf -t 8"

However I get a lot of "[E::sam_itr_next] Null iterator" lines and the final VCF has only the header lines.

Thank you, Arda

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[asylvz]

It works now, thanks @mchaisso.

[asylvz]

I'm also wondering if you have these motif set bed files relative to CHM13-T2T ref?

[mchaisso]

We just posted new motif files that are on hg38 and CHM13. If you rebuild, the help file will point you to the download.

On Mon, Jun 3, 2024 at 12:39 PM Arda Söylev @.***> wrote:

I'm also wondering if you have these motif set bed files relative to CHM13-T2T ref?

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[asylvz]

Thank you