srividya22

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

srividya22

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

srividya22

Testing Snakemake virtual memory usage

John Blischak 2014-05-14

Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).

srividya22

Testing Snakemake virtual memory usage

John Blischak 2014-05-14

Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).

srividya22

# turn a find or cut (cut delimiter, get first column) output into a list
/etc find . -name "*bash*" | xargs
cut -d, -f1 file.csv | xargs

# find a file and grep for a word in the file
find . -name "*.java" | xargs grep "Stock"

# handeling filenames which have WHITESPACE
ls *txt | xargs  -d '\n' grep "cost"

srividya22

# turn a find or cut (cut delimiter, get first column) output into a list
/etc find . -name "*bash*" | xargs
cut -d, -f1 file.csv | xargs

# find a file and grep for a word in the file
find . -name "*.java" | xargs grep "Stock"

# handeling filenames which have WHITESPACE
ls *txt | xargs  -d '\n' grep "cost"

srividya22

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
3. [Augustus](http://bio

srividya22

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
3. [Augustus](http://bio

srividya22

#!/usr/bin/env perl

=head1 NAME

    rename_genes_in_maker_gff.pl       

=head1 SYNOPSIS
 
    rename_genes_in_maker_gff.pl input_gff output_gff outputdir species  
        where input_gff is the input gff file,

srividya22

#!/usr/bin/env perl

=head1 NAME

    rename_genes_in_maker_gff.pl       

=head1 SYNOPSIS
 
    rename_genes_in_maker_gff.pl input_gff output_gff outputdir species  
        where input_gff is the input gff file,