User: Edoardo Giacopuzzi
- New User
- Brescia, Italy
- Last seen:
- 7 years, 9 months ago
- 8 years, 5 months ago
Posts by Edoardo Giacopuzzi
... Hi, I have a .bam file generated using the hg19 release of human genome downloaded from UCSC database. Now I'm trying to indentificate genomic variants using GATK UnifiedGenotyper but it returns an error cause my bam file is Lexicographically sorted. I've tried to use Picard ReorderSam function bu ...
... Thanks! It seems that adding VALIDATION_STRINGENCY option as you indicated solved the problem with Picard and now also GATK works fine. ...
... Hi, I'm trying to use GATK to identify genomic variants from my .bam file. When I use the command java -jar GenomeAnalysisTK.jar -R chr13.fa -I chr13fixed.bam -o SNP.raw.vcf -T UnifiedGenotyper -standcallconf 30.0 -standemitconf 15.0 -dcov 500 it always return this error: SAM/BAM file SAMFileRead ...
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