final result
The question is that after running GenotypeGVCF, and getting VCF file then how we can get the result for every sample we have run GenotypeGVCF. I mean if we run haplotyping for 100 samples and getting...
View Articleabout genotypegvcfs
I want to know about the algorithm which converts raw gVCF files from different samples to raw VCF by doing genotypegvcfs
View ArticleWhat are the differences in using default and custom interval list (-L) for...
I mean to say default interval list (-L) as exome region and custom interval list as designed and given by the company like agilent or illumina. What will the difference in the output generated using...
View ArticleRead Groups without known barcodes
Dear all, I am working with some barley accessions but the barcodes for the samples are not known (not publicly available). However, because the addition of the read groups is a prerequisite for BQSR...
View ArticlePicard - SortSam
Hello, I'm using Picard's SortSam tool and was wandering if I can use the same script for 2 files? Meaning, can I do something like that (script below)? What would be the separator sign? Or I would...
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9 Takeaways to help you get started with GRCh38
We are starting official support of GRCh38, a reference genome with alternate contigs. In fact, going forward all of our new projects will use GRCh38. During this transition over the coming year, we...
View ArticleGATK 3.8 log4j error
I just upgraded from GATK 3.7 to the newly released GATK 3.8 (3.8-0-ge9d806836) and I am getting a StatusLogger error: ERROR StatusLogger Unable to create class...
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How to produce GVCF files that were produced from a different reference genome?
Hi everyone. I have got my genotyped vcf file successful produced but I needed to merge them with other g.vcf files I recently received from a collaborating company. These were gzipped vcf files with...
View ArticleWhy is gatk4 GetPileupSummaries always failed ?
I used the following command /home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-launch --javaOptions "-Xmx20g" GetPileupSummaries \ -R /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta...
View ArticleGATK4 resource bundle
Hi, I was wondering if you guys are planning to release a new resource bundle with full hg38 support (+patches)? Perhaps to celebrate the release of GATK4? Thanks M
View ArticleFiltering MuTect2 output for depth of coverage
Dear GATK team, I am writing with a question about depth of coverage in the output of MuTect2 (GATK3 and GATK4). I would like to filter my somatic calls to keep only calls with sufficient depth of...
View ArticlePL
Hi, I realize PL will be normalized in this page. https://www.broadinstitute.org/gatk/guide/tagged?tag=pl However, I need the data before normalize, raw PL, where can I get it? Thanks for your help....
View ArticleOncotator error---IndexError: list index out of range
I used Oncotator (1.9.3.0) to annotate VCF file. If I run this on command line: oncotator -v --input_format VCF --output_format TCGAMAF --db-dir /share/apps/oncotator_v1_ds_April052016/ -d ....
View ArticleCannot connect to the ftp server
Hello, I tried to connect ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/ , but I got a "530 Login incorrect". Would you please check that? Thanks for your help, Henry
View ArticleGATK runtime error (READ_MAX_LENGTH must be > 0 but got 0) with 1000g bam
Hi, I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations). For most of them, when I try...
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Watch NOW!! Thor: Ragnarok Full Movie, Watch Thor: Ragnarok 2017 Full Movie Free Streaming Online with English Subtitles ready for download. Watch Thor: Ragnarok (2017) Full Movie Free on Putlocker,...
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Watch NOW!! Thor: Ragnarok Full Movie, Watch Thor: Ragnarok 2017 Full Movie Free Streaming Online with English Subtitles ready for download. Watch Thor: Ragnarok (2017) Full Movie Free on Putlocker,...
View ArticlePUTLOCKER.! Watch Thor: Ragnarok (2017) Full Online Free Movie
03.11.2017 – 123Movies-Watch! Thor: Ragnarok (2017) Full Online Free-HD INSTANT!!.WATCH Thor: Ragnarok 2017 Online free Full Movie, Watch Full!! Now Watch Thor: Ragnarok 2017 (2017) Online Free HD..NOW...
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Watch NOW!! Thor: Ragnarok Full Movie, Watch Thor: Ragnarok 2017 Full Movie Free Streaming Online with English Subtitles ready for download. Watch Thor: Ragnarok (2017) Full Movie Free on Putlocker,...
View Article++Télécharger:-Thor: Ragnarok Streaming VF '2017'~ le Film Complet VOSTFR
Télécharger.:,Thor: Ragnarok Streaming VF '2017' ~ le Film Complet VOSTFR Thor: Ragnarok 2017 Streaming VF Complet EN Français [VOST-FR] Thor: Ragnarok Films Complet Online Streaming VF En Français,...
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