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\""

brentp

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

brentp

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

brentp

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

brentp

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

brentp

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>".}

brentp

from pysam.libcalignmentfile cimport AlignmentFile

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

print samfile.reference_filename
print samfile.b == NULL

brentp

import times

type AThing = ref object
  i: int

iterator items(a:AThing): int =

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

brentp

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

brentp

import hts/vcf
import os

var gnomad_path = commandLineParams()[0]

var
  gvcf:VCF
  total:int
  mid:int