Results for "Picard"
Bio-Scripts
...ters CheckIlluminaDirectory (Picard) Asserts the val...ollectIlluminaBasecallingMetrics (Picard) Collects Illumina Basecall...pileup CheckTerminatorBlock (Picard) Asserts the p...ts reads by name FastqToSam (Picard) Con...2065 days ago
Bash script to alignment of short reads against reference genome !
...marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same criteria for marking duplicates as picard. minimap2 -ax sr -t 40 -R...1549 days ago
Bash command to install bwa, samtools, picard !
...ng transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install picard Collecting package metadata...orkshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - picard The following packages w...1545 days ago
To convert just one specific read group to fastq
...plit-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM file for each SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fast...1532 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectInsert...1326 days ago
Installing Covid19 Environment !
...######################################################################################################################################### | 100% picard-2.26.3 | 16.0 MB | #...913 days ago
