marpiech

for i in {1..22} X
do
  wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr"$i".shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz
  wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr"$i".shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz.tbi
done

wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel
bcftools concat $(ls *.vcf.gz | grep ALL | sort -k1,1V | tr -s '\n' ' ' | sed 's/ *$//g') | bgzip -c > 1kg.merged.vcf.gz

marpiech

#!/bin/bash
# Download dbsnp and update chromosome names

export DBSNP_VERSION=155

wget "https://ftp.ncbi.nih.gov/snp/archive/b$DBSNP_VERSION/VCF/GCF_000001405.39.gz"
wget "https://ftp.ncbi.nih.gov/snp/archive/b$DBSNP_VERSION/VCF/GCF_000001405.39.gz.tbi"
wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_report.txt"

cat GCF_000001405.39_GRCh38.p13_assembly_report.txt | \

marpiech

ffmpeg -i Desktop/appvideo2.mp4 -r 30 -strict -2 -vf scale=900:1200 Desktop/appvideo-ipad-2.mp4
ffmpeg -f lavfi -i anullsrc=channel_layout=stereo:sample_rate=44100 -i Desktop/appvideo-ipad-1.mp4 -shortest -c:v copy -c:a aac Downloads/appvideo-ipad-1.mp4

marpiech

import re
import sys

pattern="=[0-9]\.[0-9]*E[+-][0-9]*;"

for line in sys.stdin:
        if(re.search(pattern, line)):
                m = re.search(pattern, line)
                g = "=" + str(float(m.group(0)[1:-1])) + ";"
                line = re.sub(pattern, g, line, 0)

marpiech

Exception in thread "main" java.lang.RuntimeException: Cannot compare 'String' to 'Float'
        at ca.mcgill.mcb.pcingola.snpSift.lang.expression.Expression.compareTo(Expression.java:51)
        at ca.mcgill.mcb.pcingola.snpSift.lang.condition.Lt.eval(Lt.java:21)
        at ca.mcgill.mcb.pcingola.snpSift.lang.condition.Or.eval(Or.java:18)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.evaluate(SnpSiftCmdFilter.java:191)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:356)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:322)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:233)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:60)

marpiech

# removeVcfInfoField.py script removes selected field from the INFO inside vcf
# usage: python removeVcfInfoField.py [vcf file] [name of the field] > [output vcf]
# 
# example: python removeVcfInfoField.py input.vcf AO > output.vcf

import sys

def removeField(line, field):
        values = line.split()
        INFO = values[7]

marpiech

# create sample bed file
echo -e "chr1\t1000\t2000\nchr2\t1000\t2000" > sample.bed

# use bedtools to extend bed by 100 bases each side
# use -l to extend on the left or -r on the right
bedtools slop -i sample.bed -g ~/tools/bedtools/genomes/mouse.mm9.genome -b 100

# alternatively use bedops
# use --range argument to specify LEFT:RIGHT extension
bedops --range 100:100 --everything sample.bed

marpiech

tmap mapall -f /tmp/tmap/genome.fa -r /results/analysis/output/Home/Auto_user_PR1-10-Ion_RNA_-_Whole_Transcriptome_-_neurons_32_024/plugin_out/FastqCreator_out/RNA_Barcode_None_001_R_2013_06_27_09_04_01_user_PR1-10-Ion_RNA_-_Whole_Transcriptome_-_neurons_Auto_user_PR1-10-Ion_RNA_-_Whole_Transcriptome_-_neurons_32.fastq -i fastq stage1 map4 > tmap.sam

marpiech

	<dependencies>
 
		<!-- Spring 3 -->
		<dependency>
			<groupId>org.springframework</groupId>
			<artifactId>spring-core</artifactId>
			<version>${spring.version}</version>
		</dependency>
 
		<dependency>

marpiech

<!--?xml version="1.0" encoding="UTF-8"?-->
<project xsi:schemalocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

  <modelversion>4.0.0</modelversion>
 
   <groupid>org.cremag</groupid>
   <artifactid>spring-tutorial</artifactid>
   <version>1.0</version>
 
   <name>Spring security</name>