This pipeline is a copy of the pipeline on bitbucket with additions about how to use this pipelines for human cells. based on the following: https://bitbucket.org/tychoCanterCremers/batch-ge_pipeline/src/master/
- Genotyping SNPpanel using MIPS pipeline Nijmegen
- Input needed:
- Illumins SampleSheet.csv: samples with "smMIPS" as Sample_project will be used, rest will be ignored
- Design 70mer file
- SNPpanel in VCF format
- Copy 'localconfiguration.example.xml' to 'localconfiguration.xml' inside the repo and fill in the necessary info
- Then run the main script: perl run.MIPS.pl
- Dependencies (defined in mainconfiguration.xml):
- bwa, cutadapt v.1.15, java, GATK v3.5, Python3.6 (installed on cluster)
- Set up to run as cronjob
Missense mutation = desired edit:
Example:
Human (GRCh38.p13): CACNA1Cc.989C>T
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Transcript: CACNA1C-204 ENST00000347598.9
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Chr12 2493262 = mutation site
Adapted Batch-GE “zebrafish script”
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To provide:
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Genome for reference
- e.g.: “GRCh38/hg38”
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Genomic Region Of Interest (ROI) – unique per sgRNA
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mutation site in the middle
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add 10-15nt down- or upstream from cut site (related to sgRNA)
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add 10-15nt down- or upstream from mutation site
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Total length = max 40nt
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e.g.: chr12 2493244 - 2493277
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Repair sequence:
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= desired mutation; presence is required to count as knock-in (KI) read
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( ) = silent mutations; presence is optional to count as KI read
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| = cut site (as example): CAGTGCCAGAA(T)G|G(A)A[T]GGTGTGCAAGCC
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Final repair sequence e.g.: CAGTGCCAGAA(T)GG(A)A[T]GGTGTGCAAGCC
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When script is finished => output_mail.txt
- Each row contains: Sample_ID; total_reads; InDel reads; KI reads
Small insertion or deletion (max 50bp) = desired edit:
After Batch_GE “zebrafish_script” use "Variants.INS.Seq.annotated" and "output_mail.txt" to run cardio_zebrafishpipeline/BATCH-GE_intended_INS_finder/src/BATCH-GE_INS_finder.py, more information and a README about this script can be found in the same directory.