edawson

Functions:

# encoding: ACTG

def nuc2int_nochecking(b):
    return (ord(b) >> 1) & 3, True
    
def nuc2int_if(b):
    if b == 'a' or b == 'c' or b == 'g' or b == 't' \

or b == 'A' or b == 'C' or b == 'G' or b == 'T':

edawson

#############
## Download the 30X hg19-aligned bam from Google's public sequencing of HG002
## and the respective BAI file.
#############

wget https://storage.googleapis.com/brain-genomics-public/research/sequencing/grch37/bam/hiseqx/wgs_pcr_free/30x/HG002.hiseqx.pcr-free.30x.dedup.grch37.bam
wget https://storage.googleapis.com/brain-genomics-public/research/sequencing/grch37/bam/hiseqx/wgs_pcr_free/30x/HG002.hiseqx.pcr-free.30x.dedup.grch37.bam.bai

edawson

#!/bin/bash

########################
## In this gist, we'll reuse the commands from our 3.6 tutorial to align reads and generate BAM files.
## Check out the full post at https://medium.com/@johnnyisraeli/accelerating-germline-and-somatic-genomic-analysis-of-whole-genomes-and-exomes-with-nvidia-clara-e3deeae2acc9
and Gists at:
## https://gist.github.com/edawson/e84b2785db75d3c0aea9cc6a59969d45#file-full_pipeline_and_data_prep_parabricks3-6-sh
## and 
## https://gist.github.com/edawson/e84b2785db75d3c0aea9cc6a59969d45#file-step_1_align_reads_parabricks3-6-sh
###########

edawson

#!/bin/bash

## Download the HG002 30X BAMs, kindly sequenced and shared by Google
gsutil cp gs://brain-genomics-public/research/sequencing/fastq/hiseqx/wgs_pcr_free/30x/HG002.hiseqx.pcr-free.30x.R1.fastq.gz .
gsutil cp gs://brain-genomics-public/research/sequencing/fastq/hiseqx/wgs_pcr_free/30x/HG002.hiseqx.pcr-free.30x.R2.fastq.gz .

## Download GRCh38
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
gunzip GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

edawson

#Example 1:

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process AFcalc {

    """
    echo  '${params.str}'

edawson

#include <sys/mman.h>
#include <fcntl.h>
#include <unistd.h>
#include <cuda_runtime.h>

#include <cerrno>
#include <cstring>
#include <memory>
#include <stdexcept>

edawson

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <htslib/sam.h>

int main(int argc, char *argv[]){
	
	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
	bam1_t *aln = bam_init1(); //initialize an alignment

edawson

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

edawson

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

edawson

## Tasks are upper camel-cased
task CheckSex{
    File sampleBAM
    File sampleIndex
    
    ## Optional parameters receive a '?' after the type
    Int? diskGB
    
    ## select_first can be used to set default values
    diskGB = select_first([diskGB, 100])