This week, three lucky GATK team members are teaching an invited workshop at Mahidol University in Bangkok, Thailand! The slide decks for each day will be available at the start of the day here in the GSA dropbox. After the workshop, all materials will be available in the Presentations section of the GATK website as usual.


Comment on this article in the forum



At a glance



Follow us on Twitter

GATK Dev Team

@gatk_dev

@iskander @NJL_NGS Treat them like any other read, no special handling. Problems arise in CIGAR functions that don’t know how to handle Ns.
7 Dec 16
@iskander @NJL_NGS By default we error out. Possible to override using -U ALLOW_N_CIGAR_READS but tool may crash. Is unsupported usage.
7 Dec 16
RT @geoffjentry: How @WDL_dev empowers a biochemist w/o programming background to perform large scale genomics analyses: https://t.co/BxAnK
6 Dec 16
@iskander @NJL_NGS Not aware of any, sorry.
5 Dec 16
@NJL_NGS @iskander No, GATK tools don't handle Ns in CIGAR, splitting is obligatory. See RNAseq guidelines in docs for more details.
5 Dec 16

Our favorite tweets from others

Currently in a time-out for saying that duck fat had a certain "je ne sais quack" at the thanksgiving dinner table.
25 Nov 16
@dgmacarthur @BioMickWatson @StevenNHart @splon There's even a shop near Broad that apparently fixes Hail code erro… https://t.co/IZ4BcgRZYE
19 Nov 16
I'm very happy to be at GATK Workshop hands on with @gatk_dev ! There's always something to learn. Tip: there is free coffee. Lol
8 Nov 16
Have recently begun to think of slide editing as ‘downsampling my slides’. I suspect this indicates something is wrong with me.
1 Nov 16
See more of our favorite tweets...
Search blog by tag

appistry ashg ashg16 benchmarks best-practices bug bug-fixed cancer cloud cluster cnv collaboration commandline commandlinegatk community compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fix forum gatk3 gatk4 genotype genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm intel java8 job job-offer jobs license meetings mendelianviolations mutect mutect2 ngs outreach pairhmm parallelism patch performance phone-home picard pipeline plans ploidy polyploid poster presentations printreads profile promote release release-notes rnaseq runtime saas script search sequencing service slides snow speed status sting support syntax talks team terminology third-party-tools topstory troll tutorial unifiedgenotyper vcf-gz version-highlights versions vqsr wdl webinar workflow workshop