Changes between Version 25 and Version 26 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
10/31/25 14:16:29 (3 days ago)
Author:
kdesilva
Comment:

--

Legend:

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  • SOPs/variant_calling_GATK

    v25 v26  
    3333\\
    34344 - '''Align reads to genome with [[http://bio-bwa.sourceforge.net/bwa.shtml|bwa]]'''
    35   * bsub "bwa aln /path/to/genome/bwa/genome Reads_1.fq > Reads_1.sai"
    36   * bsub "bwa samse /path/to/genome/bwa/genome Reads_1.sai  Reads_1.fq > Reads_1.bwa.sam"
     35  * sbatch --job-name=bwa_aln_1 --mem=16G --wrap="bwa aln /path/to/genome/bwa/genome Reads_1.fq > Reads_1.sai"
     36  * sbatch --job-name=bwa_samse_1 --mem=16G --wrap="bwa samse /path/to/genome/bwa/genome Reads_1.sai  Reads_1.fq > Reads_1.bwa.sam"
    3737\\
    38385 - '''Convert SAM to BAM, sort, and index''' with BaRC's streamlined [[http://samtools.sourceforge.net/samtools.shtml|samtools]] commands
    39   * bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl Reads_1.bwa.sam
     39  * sbatch --job-name=SAM2BAM --wrap="/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl Reads_1.bwa.sam"
    4040\\
    41416 - '''Mark duplicates''' (multiple identical reads mapped to the same location) \\