Brent Pedersen brentp

fgbio -> annotated-filtered-vcf

run fgbio via netxflow:

echo "sample,fastq_1,fastq_2,read_structure" > sheet.csv
for f in /scratch/ucgd/lustre-work/quinlan/data-shared/datasets/spermseq/final_seq/Fastq/merged/*_R1*.fastq.gz; do
   # s=$(basename $f _R1.merged.fastq.gz)
   # R2=${f/_R1/_R2}
   # echo "$s,$f,$R2,\"$structure $structure\""

Need: A simple way to draw pedigrees. This R script will draw a PNG per family in a pedigree file.

Some answers here: https://twitter.com/brent_p/status/1222196118563381248 and others off-line:

peddraw using graphviz/dot from pubsnips
drawmyped using d3 from Sam

using dot/graphviz

Also see: https://twitter.com/Yutaka__Masuda/status/1222214145233182720

nim c -d:danger -d:release -r abs.nim > abs.txt
mkdir -p pngs
python abs.py
rm -f pngs/NA*
rm -f pngs/HG*
convert -delay 25 pngs/*.png -loop 0 abs.gif

	import futhark
	import std/typetraits

	type CFile* = typeof(File.pointerBase)

	importc:
	sysPath "/usr/lib/clang/13/include"
	path "./WFA2-lib"
	"wavefront/wavefront_align.h"
	rename FILE, CFile

	WGS:
	http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGDP/
	from: "Insights into human genetic variation and population
	history from 929 diverse genomes"


	WGS, exome, RNA-Seq
	many samples available from St Jude via DNA Nexus
	https://platform.stjude.cloud/requests/cohorts


	import bitops

	{.passC:"-mavx512f -mavx512vl -mavx512bw -mpopcnt"}
	{.passL:"-mavx512f -mavx512vl -mavx512bw -mpopcnt"}

	when defined(vcc):
	{.pragma: x86, noDecl, header:"<intrin.h>".}
	else:
	{.pragma: x86, noDecl, header:"<x86intrin.h>".}

	from pysam.libcalignmentfile cimport AlignmentFile

	cdef AlignmentFile samfile = AlignmentFile("../normal.bam", "rb")

	print samfile.reference_filename
	print samfile.b == NULL

	import times

	type AThing = ref object
	i: int

	iterator items(a:AThing): int =

	when defined(dodefer):
	defer:
	a.i = 11

	import times
	import intsets
	import tables
	import sets

	# cardinality for builtin sets is slow.
	# nim c -d:release -r t.nim
	# vs
	# nim c -d:card -d:release -r t.nim

	import hts/vcf
	import os

	var gnomad_path = commandLineParams()[0]

	var
	gvcf:VCF
	total:int
	mid:int