SSH123
- Total activity 16
- Last activity
- Member since
- Following 0 users
- Followed by 1 user
- Votes 0
- Subscriptions 3
Activity overview
Latest activity by SSH123-
SSH123 commented,
Hi, Genevieve, Thanks very much for the information you provided. I've created a chain file based on UCSC Genome Browser. Can you please help me to check it? Thanks, SSH123
-
SSH123 commented,
Hi, Genevieve, Thanks for reviewing my question. I was trying to load the M2 VCF files into Gemini and run some queries like what I did with Varscan2 VCF files. Somehow it didn't work. The error co...
-
SSH123 created a post,
MuTect2 Phasing tags (PGT:PID:PS:) in FORMAT column: How to avoid/remove them?
AnsweredHi, there, I used M2 and followed the SOP and like many others came across this phasing tags (PGT:PID:PS:) insertion problem. This unorthodox GT "0|1:10,2:0.216:12:6,2:3,0:0|1:161166384_G_T:1611663...
-
SSH123 commented,
Hi, Genevieve, Thanks for your help. I've solved this problem. Basically, it can be done by using -XL somatic-b37-final_centromere_hg19.seg. Otherwise, it can be downloaded from UCSC Table Browser ...
-
SSH123 created a post,
Where do I find a b37/hg19 WGS interval_list?
AnsweredHi, I'm following steps to create a GenomicsDB from the normal Mutect2 calls. It requires a -L interval_list for the test, which cannot be missed. My data is a WGS provided by BGI. Where do I find ...
-
SSH123 commented,
Hi, Genevieve, you were right: picard successfully lifted gnomad after I increased java max heap. And mutect also worked. Do you think somebody is going to update the chain file soon? Because there...
-
SSH123 commented,
Hi, Genevieve, It failed after 42 minters. The output vcf file is empty. No index file was made. Please see code and slurm.out below. Thanks. Code: java -jar picard.jar LiftoverVcf \I=reference/som...
-
SSH123 commented,
Hi, Genevieve, It'd be nice if you could update the chain file. This particular chain is not listed in Golden Gate repository. Directly downloading from the https didn't work for me. Copying and pa...
-
SSH123 commented,
Hi, Genevieve, I changed reference to ucsc.hg19.fasta. Similar error except this time reference contigs = [chrM, chr1...] and features contigs = [1, 2...]. So, it looks the ucsc.hg19.fasta, my bam ...
-
SSH123 commented,
Thanks for your patience, Genevieve. But it looks in that resource you pointed to the file could not work for hg19. See below for the code and error. It is an obvious b37 to hg19 contig error. Code...