mkatari-bioinformatics-august-2013-gatknotes
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| mkatari-bioinformatics-august-2013-gatknotes [2016/08/11 12:28] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2016/08/17 08:37] (current) – mkatari | ||
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| bowtie2-build PTC_Human.fasta PTC_Human | bowtie2-build PTC_Human.fasta PTC_Human | ||
| samtools faidx PTC_Human.fasta | samtools faidx PTC_Human.fasta | ||
| - | picard CreateSequenceDictionary.jar \ | + | picard CreateSequenceDictionary \ |
| | | ||
| | | ||
| Line 261: | Line 261: | ||
| < | < | ||
| GenomeAnalysisTK \ | GenomeAnalysisTK \ | ||
| - | -R PTC_Human.fasta | + | -R PTC_Human.fasta |
| -T VariantsToTable \ | -T VariantsToTable \ | ||
| -V PTC_human.gatk.vcf \ | -V PTC_human.gatk.vcf \ | ||
| Line 277: | Line 277: | ||
| -o PTC_human.gatk.filter.vcf \ | -o PTC_human.gatk.filter.vcf \ | ||
| --variant PTC_human.gatk.vcf \ | --variant PTC_human.gatk.vcf \ | ||
| - | --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore > | + | --filterExpression " |
| - | --filterName | + | --filterName mannyfilter |
| </ | </ | ||
mkatari-bioinformatics-august-2013-gatknotes.1470918484.txt.gz · Last modified: 2016/08/11 12:28 by mkatari