johnsonz

smoove annotation

3

Hi, @brentp, @lindenb Thanks for your great work ! There was a problem with the annotation ``` smoove annotate --gff silkie_end.gff3.gz 26indiv_ZW-smoove.genotyped.vcf.gz | bgzip -c > 26indiv_ZW-smoove.genotyped.anno.vcf.gz (smoove) [poultrylab1@pbsnode01 sk_as_ref_118_indev_bam]$...

Why Partition contigs into only one group ?

18

Hi Dr.zhang Thanks your great work in ALLHIC ! I am following the step in , and mapping my reads by using the code...

Why there is only one group?

1

Hi @tangerzhang After parition, there is only one group. This is my code ``` parallel -N2 -k -j 4 "bwa-mem2.avx512bw mem -R '@RG\tID:{1}\tPL:illumina\tSM:{1}' -t 8 ${r} {1} {2} | samtools...

31个样本SV如何合并到一个vcf文件

2

尊敬的周老师@YaoZhou89 请问在如下步骤中，多个个体以什么方式合并到一个vcf中，多个样本合并还是融合到一个样本？  这里的cleanSV行使了什么功能？ 另外，在如下步骤中，如果我的流程中不涉及使用多个SV calling软件，只用了一个软件，我可以不使用这个步骤来对SV去重吗？  敬上 强森

Purge dups ?

8

Hi @AntonBankevich ? Is there need to purge haplotype duplication of the output assebmly ? As far as I know, Canu and HiFiasm needs another run of purge_dups. Thanks in...

Fail to build

4

Dear @adamnovak, I came cross an error when I build sequenceTubeMap ``` (yarn) [poultrylab1@pbsnode01 sequenceTubeMap]$ yarn install yarn install v1.22.19 warning package-lock.json found. Your project contains lock files generated by...

Hi @ypriverol Its nice to integrate Chromap into this pipeline, Did you put that in plan？ BEST Johnsonz

No such file

17

``` (nanome) [poultrylab1@pbsnode01 nanome]$ nextflow run TheJacksonLaboratory/nanome -profile test,docker N E X T F L O W ~ version 21.10.0 Launching `TheJacksonLaboratory/nanome` [chaotic_hamilton] - revision: c181f907e9 [master] NANOME - NF...