duphold
duphold copied to clipboard
brentp
don't get DUP'ed or DEL'ed by your putative SVs.
Any suggestions for this error? ``` tail smoove_duphold_ont_manta.sh.o3870689 [smoove] 2022/03/31 11:14:06 [duphold] finished [smoove] 2022/03/31 11:14:07 [duphold] finished [smoove] 2022/03/31 11:14:07 [duphold] finished [smoove] 2022/03/31 11:14:07 [duphold] finished [smoove] 2022/03/31...
Hi @brentp I have a question about missing insertion variants. I used sample HG002 for variant calling with smoove using the command below. But it seems strange to me that...
Hi, I used duphold on some VCFs containing SVs called with Sniffles where the alignment was done using minimap2. The data used is all nanopore longread data. I was wondering...
Hello @brentp, Thank you for this tool! I had e.g. errors like this [duphold] couldn't find sample:sqcudn971184 in snps vcf which had:sqcudn971184.187147 due to bam file and snps VCF file...
Hello @brentp, Thanks for this awesome tool! It would be great, if duphold could be used to compute (B Allele freq /DHGT field) from gVCF files(where non-variant sites are represented...
It would be great that the Duphold stats be extended to insertions such as those generated by Manta. Duphold has been great for the QC of DEL and DUP FP...
Hi Brent, I have calls from 4 SV-callers for all my 5 samples then ran DUPHOLD before merging. In 2/5 samples, DUPHOLD failed on predictions from 1 SV-caller (SMOOVE), the...
Hi, DHSP (count of discordant reads that support the event) is very useful when we are evaluating a deletion. Why we do not have DHSP for duplications also? Could you...
I am running duphold on about 5000 crams. About 120 or so are finishing but the output vcf is not complete. It ends prematurely near the end of chromosome 22....
Hi, I used duphold to filter out false positives and it works pretty well. Thanks a lot for making this nice programme! I was thinking that Duphold can be useful...
