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nh13 / AGBT2025.ics
Created February 21, 2025 21:23
Calendar for AGBT 2025
BEGIN:VCALENDAR
VERSION:2.0
PRODID:ics.py - http://git.io/lLljaA
BEGIN:VEVENT
DESCRIPTION:Session: Plenary Session: Genetics (Len Pennacchio\, Lawrence Berkeley National Laboratory and DOE Joint Genome Institute\, Session Chair)\nTitle: ” Genomics – looking back\, looking forwards. A view from EMBL”\nSub-title: Ewan Birney\nLocation: Calusa Ballroom 1-7\nDate: Sunday\, February 23\nTime: 5:40 p.m. – 6:10 p.m.\n
DTEND:20250223T231000Z
LOCATION:Calusa Ballroom 1-7
DTSTART:20250223T224000Z
SUMMARY:Plenary Session: Genetics ” Genomics – looking back\, looking forwards. A view from EMBL” Ewan Birney
UID:[email protected]
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nh13 / README.md
Created January 10, 2025 20:31

Tests for pybwa

mamba create -y -n pybwa setuptools cython python=3.11 poetry=1.8 snakemake-minimal=7 defopt samtools bwa pysam fgpyo sra-tools
conda activate pybwa
snakemake --cores $(nproc) --snakefile Snakefile --directory output
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nh13 / README.md
Created October 25, 2023 07:23
Split the value in a SAM tag

Split a SAM tag value and store in multiple SAM tags

This is motiviated by fulcrumgenomics/fgsv#25 whereby the be tag stores a semi-colon delimited list of break end values, and we want each value to be in their own tag. Supports where the case where the be tag may contain multiple such delimited values, each seperated by a different delimiter (in this case a comma).

python split_sam_tag.py \
  --in-bam fgsv.bam \
  --out-bam split.bam \
 --in-tag be \
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nh13 / gist:beae4393fd3c9ad75f514dfa092b6cce
Last active January 12, 2021 01:38
HARD TRIM
pigz -d -c in.fastq.gz |
| awk 'BEGIN {LN=0; } { if (LN == 1 || LN == 3) { print substr($0, 0, 26) } else { print $0 } ; if (LN == 3) { LN = 0 } else { LN++ } }' \
| pigz -c - > out.fastq.gz
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nh13 / test_snakemake.py
Created October 30, 2020 18:01
from collections import defaultdict
from pathlib import Path
from typing import Any
from typing import Callable
from typing import Dict
from typing import List
from typing import Optional
import snakemake
@nh13
nh13 / aliases.sh
Created August 9, 2020 19:01
# Delimited-data files: no empty columns please
function columnit { column -t $1 | less -S; }
function tabit { column -t -s $'\t' $1 | less -S; }
# Delimited-data files: empty columns values are nasty
function columnit-empty { cat $1 | sed -E 's_'$'\t'$'\t''_'$'\t''NA'$'\t''_g' | column -t | less -S; }
function tabit-empty { cat $1 | sed -E 's_'$'\t'$'\t''_'$'\t''NA'$'\t''_g' | column -t -s $'\t' | less -S; }
# Show me the money grep, now
function grep-nobuff { gstdbuf -o0 grep $@; }
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nh13 / michael_hoffmans_super_special_wishmaker.dict
Last active May 22, 2020 02:31
Michael Hoffmans Super Special Wishmaker
@HD VN:1.6
@SQ SN:chr1 LN:249250621 am:1 ga:CM000663.1 sn:1 ra:NC_000001.10 un:chr1 AN:1,CM000663.1,NC_000001.10 sr:assembled-molecule
@SQ SN:chr2 LN:243199373 am:2 ga:CM000664.1 sn:2 ra:NC_000002.11 un:chr2 AN:2,CM000664.1,NC_000002.11 sr:assembled-molecule
@SQ SN:chr3 LN:198022430 am:3 ga:CM000665.1 sn:3 ra:NC_000003.11 un:chr3 AN:3,CM000665.1,NC_000003.11 sr:assembled-molecule
@SQ SN:chr4 LN:191154276 am:4 ga:CM000666.1 sn:4 ra:NC_000004.11 un:chr4 AN:4,CM000666.1,NC_000004.11 sr:assembled-molecule
@SQ SN:chr5 LN:180915260 am:5 ga:CM000667.1 sn:5 ra:NC_000005.9 un:chr5 AN:5,CM000667.1,NC_000005.9 sr:assembled-molecule
@SQ SN:chr6 LN:171115067 am:6 ga:CM000668.1 sn:6 ra:NC_000006.11 un:chr6 AN:6,CM000668.1,NC_000006.11 sr:assembled-molecule
@SQ SN:chr7 LN:159138663 am:7 ga:CM000669.1 sn:7 ra:NC_000007.13 un:chr7 AN:7,CM000669.1,NC_000007.13 sr:assembled-molecule
@SQ SN:chr8 LN:146364022 am:8 ga:CM000670.1 sn:8 ra:NC_000008.10 un:chr8 AN:8,CM000670.1,NC_000008.10 sr:assembled-molecule
@SQ SN:chr9 LN:14121343
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nh13 / primer_pairs_example.sam
Last active May 21, 2020 07:20
Example SAM file with Primer Pairs
@HD VN:1.6 GO:query SO:unsorted SS:unsorted:template-coordinate
@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:hg38 UR:ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz SP:Homo sapiens AN:NC_000001.11,CM000663.2
@SQ SN:chr2 LN:242193529 M5:f98db672eb0993dcfdabafe2a882905c AS:hg38 UR:ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz SP:Homo sapiens AN:NC_000002.12,CM000664.2
@SQ SN:chr3 LN:198295559 M5:76635a41ea913a405ded820447d067b0 AS:hg38 UR:ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz SP:Homo sapiens AN:NC_000003.12,CM000665.2
@SQ SN:chr4 LN:190214555 M5:3210fecf1eb92d5489da4346b3fddc6e AS:hg38 UR:ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz SP:Homo sapiens AN:NC_000004.12,CM00066
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nh13 / add_rg_per_read.sc
Created April 17, 2020 03:21
Add a read group (and sample) per read in a SAM/BAM
import $ivy.`com.fulcrumgenomics::fgbio:1.1.0`
import com.fulcrumgenomics.FgBioDef._
import java.nio.file.{Path, Paths}
import com.fulcrumgenomics.commons.util.{LazyLogging, Logger}
import com.fulcrumgenomics.util.ProgressLogger
import com.fulcrumgenomics.bam.api._
import htsjdk.samtools.SAMReadGroupRecord
// So that a [[Path]] can be built from a [[String]] on the command line
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nh13 / snakefile.smk
Created April 10, 2020 22:48
import enum
from typing import List
from pathlib import Path
class Alignment(enum.Enum):
BWA = 1
Bowtie = 2
class VariantCalling(enum.Enum):