EXCAVATE-HT Examples
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Example run: Generating a paired dual-gRNA library 
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Generating paired dual-gRNAs targeting heterozygous SNVs in an individual cell-line in the MFN2 locus, for the SpCas9 enzyme, 
paired via "random" method (all gRNA targeting different SNPs paired together) in the locus. Off-targets enabled,
--download-hg38-index will automatically download required hg38 indexes for off-targets analysis.

.. code-block:: bash

   excavate-ht generate \
     --vcf cellline.vcf.gz \
     --var_type cell-line \
     --chrom_fa chrom1.fasta \
     --locus chr1:11975541-12019490 \
     --cas SpCas9 \
     --pairing-method r \
     --off-targets \
     --download-hg38-index \
     --summary \
     -o paired_gRNA_output_folder


Example run: Generating a single-gRNA library, editing it, then pairing to create a dual-gRNA library 
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Generaing single-gRNAs targeting heteroyzgous SNVs in an individual cell-line and common SNPs present
in the 1000 genomes project, in the MFN2 locus, for a custom 5prime PAM sequence. Off-targets enabled, 
pre-built genome and chromosome index file prefixes provided using --genome-index-prefix and --chrom-index-prefix flags

.. code-block:: bash

   excavate-ht generate \
     --vcf cellline.vcf.gz,1000genomes_chrom1.vcf.gz \
     --var_type cell-line,population \
     --chrom_fa chrom1.fasta \
     --locus chr1:11975541-12019490 \
     --pam-list TRTV \
     --orient 5prime \
     --off-targets \
     --genome-index-prefix /path/to/hg38genome_index_prefix/genome_bt1 \
     --chrom-index-prefix /path/to/chrom1_index_prefix/genome_bt1 \
     --summary \
     -o single_gRNA_output_folder

This sgRNA library can now be manually edited. gRNA with many off-target sites, as revealed by the --off-targets analysis option, 
can be filtered out, and screening controls such as non-targeting gRNA or experimentally verified gRNA can be added in.

After you have the final library of all single-gRNA you want included in your library/screen, you can pair up this user-input 
sgRNA library to create a library of paired dual-gRNA elements, using excavate-ht pair. We will pair up gRNA about a fixed-point in the MFN2 locus.  

.. code-block:: bash

   excavate-ht pair \
     --input-library final_sgRNA_MFN2_library.csv
     --pairing-method fp\
     --fixed-points-list 11976861 \
     -o paired_MFN2_library