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':
#!/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 |
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':
#!/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 | |
########### |
############# | |
## 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 | |
#Example 1: | |
#!/usr/bin/env nextflow | |
params.str = 'Hello world!' | |
process AFcalc { | |
""" | |
echo '${params.str}' |
#include <sys/mman.h> | |
#include <fcntl.h> | |
#include <unistd.h> | |
#include <cuda_runtime.h> | |
#include <cerrno> | |
#include <cstring> | |
#include <memory> | |
#include <stdexcept> |
#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 |
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.
chmod a+x vcfsort.sh | |
vcfsort.sh trio.trim.vep.vcf.gz |