huangl07

like the top manual，could you please add users information

outgroup

4

dear yu is there anyway to set an outgroup for draw a tree？ thanyou！

multi-sample genernate pipeline

13

dear Manta support: I was used to analysis `configManta.py --bam=SRR5739119.mkdup.bam --bam=SRR5739120.mkdup.bam --bam=SRR5739121.mkdup.bam --bam=SRR5739122.mkdup.bam --bam=SRR5739123.mkdup.bam --referenceFasta=../Genome/ref.fa --runDir=SV` and it turns out Error like this: ``` [2018-12-17T13:55:49.944212Z] [localhost.localdomain] [28400_1] [TaskManager] [ERROR] Failed...

System.Collections.Generic.KeyNotFoundException: The given key '*.bam' was not present in the dictionary.

4

dear canvas support I have run a canvas worksh like dotnet $prefix/Canvas-1.39.0.1598+master_x64/Canvas.dll Germline-WGS --bam=FAM1201802.mkdup.bam --sample-b-allele-vcf=out.recode.vcf -r Genome/ref_1/ref/ref/Sequence/WholeGenomeFASTA/genome.fa -g Genome/ -o FAM1201802-cnv --sample-name=FAM1201802 --filter-bed=1.bed but it turns out 2018-12-12T10:53:03+08:00, 2018-12-12T10:53:03+08:00,Running checkpoint...

Index Error: index 1 is out of bounds for axis 1 with size 1

1

Hi like the code show error ` xpclr --input /mnt/ilustre/users/dna/Development/SelectGeneFlow/new/work/71/a224da5aff8422edac251f43d541e5/pop.filtered.vcf.gz --samplesA /mnt/ilustre/users/dna/Development/SelectGeneFlow/new/work/6e/a6013b8945088516617de514b02949/1.txt --samplesB /mnt/ilustre/users/dna/Development/SelectGeneFlow/new/work/6e/a6013b8945088516617de514b02949/3.txt --out ./1_3-sca176.xpclr --chr sca176 --size 100000 2022-06-17 08:01:00 : INFO : running xpclr v1.1.2 2022-06-17 08:01:00...

Error in while (change > conv) { : missing value where TRUE/FALSE needed

11

hello, I got errors when I use some gene express matrix by counts when I use Combat my script is : `sample

fill-tags issue for specific sample name

4

hello， I have a vcf file， which sample name is like “A1”，“C1”； when I using the filter-tag plugins，it turns out error for group files，maybe you could rewrite the check code...

gmhmmp Segmentation fault

1

when we use the braker3 to do an Arthropoda species，it rurns out this [itr_0.zip](https://github.com/Gaius-Augustus/BRAKER/files/13622214/itr_0.zip) [gms.log](https://github.com/Gaius-Augustus/BRAKER/files/13622202/gms.log) /mnt/lustre/users/sanger-dev/sg-users/pengyu.guo/app/braker3_relay/GeneMark-ETP-main/bin/gmst/gmhmmp -p 0 sequence -m /mnt/lustre/users/sanger-dev/sg-users/pengyu.guo/app/braker3_relay/GeneMark-ETP-main/bin/gmst/MetaGeneMark_v1.mod -o itr_0.lst Error on last system call, error code...

hello, thanks for your Outstanding software， but I wander is there someway to accelerate the software？ I have about 1000 samples to do and why it can't support CRAM format