duphold

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Error running Duphold, "expected AD field in snps VCF"

12

I'm running duphold v 0.2.1 The command I am running is: ~/install_crap/duphold/duphold -v ./results.vcf.gz -b /efs/WGS/data/WGS/ILMN_exptA/b37/KC_downsampledBAM_and_VCF/NA24385/40x/S7508/NA24385.40x.S7508.aligned.deduped.sort.bam -f /efs/WGS/data/reference/human/human_g1k_v37_modified.fasta/human_g1k_v37_modified.fasta -s ./x.vcf.gz -t 96 -o ./duphold.vcf It spins for a while, then...

johnemajor

How is DHSP computed?

2

Hi Brent, How is the count of spanning read-pairs (DHSP) defined in duphold? Is it the number of discordantly aligned read pairs that flank a deletion event? If so, I...

raul-w

Not every line was annotated?

2

Hi, I use duphold to calculate SV depth, but I find that not every vcf line was annotated with the tags, how to interpret this situation? ``` chr17 57986589 7_2...

xiucz

using duphold on a multisample trio VCF file

2

Hi, I have a multisample trio VCF file generated using Oxford Nanopore long read data. Is there any way where duphold can be used on a multisample VCF file? Regards,...

prasundutta87

Cutoff for duplications

6

The cutoff for deletions is DHFFC 0.7. What is the recommended DHBFC cutoff for duplications?

robertzeibich

Should the tool duphold also work on small deletions <50bp?

4

I got 12 true positive deletions with deletion sizes from 1 to 16bp. However, only for the deletion with a size of 16, I got a DHFFC < 0.7. Seems...

robertzeibich

svtype = variant.info.get("SVTYPE", "SV")

2

I am getting the following error and I am not sure how to go around this. I used the following command to annotate the my vcf. `duphold -v macope2_sorted.vcf -b...

Jokendo-collab

IndexDefect error in Version 0.2.1 - call for update in bioconda

1

Hi @brentp , Thanks for writing this useful tool. I installed `smoove 0.2.8` through bioconda, then used `duphold` in it (the version is 0.2.1) to calculate adjacent read depth of...

sunjh22