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

*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

Identify a directory which does not contain a particular file
find base_dir -mindepth 2 -maxdepth 2 -type d '!' -exec test -e "{}/cover.jpg" ';' -print

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

Links: 
http://quinlanlab.org/tutorials/bedtools/bedtools.html

Use Case 1:  Given a.bam and b.regions.bed. how to get the parts of b.regions.bed that are not covered by a.bam?
Answer:
bedtools genomecov -ibam aln.bam -bga \
               | awk '$4==0' |
               | bedtools intersect -a regions -b - > foo
               
Option -bga	Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: “grep -w 0$” to the output.

srividya22

#!/usr/bin/env python
# Script to identify gaps regions in an assembly
# input : fasta 
# output : bed
# usage : get_gap_postions.py fasta bed
# Import necessary packages
import argparse
import re
from Bio import SeqIO

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