My 30xWGS .vcf appears matching a bit with neanderthal/denisovan.
wyet...@icloud.com
Any place to compare my .vcf results with other folks? Only have YSEQ, Sequencing and Nebula Genomics results from relatives.
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&position=default&g=ancient
http://hgdownload.soe.ucsc.edu/gbdb/hg38/ancient/
When GRCh38 are in a or b and 30xWGS
(Nebula Genomics for NBU3T732.vcf)
a=neanderthal.hg38.filt.vcf.gz
b=denisovan.hg38.filt.vcf.gz
a != b != chr NBU3T732.vcf
150838 10323 148139 11159 chr1 397095
154706 10097 152773 10952 chr2 391272
132371 8386 130385 8994 chr3 325993
140853 8019 136760 8745 chr4 343746
117374 7234 116007 7883 chr5 289330
127344 7719 127116 8513 chr6 307642
109952 7084 107307 7714 chr7 277904
99667 5975 97983 6436 chr8 240558
81695 5150 80289 5705 chr9 221607
101050 6421 98912 7168 chr10 253095
97901 5963 96343 6530 chr11 240632
92270 6261 88574 6836 chr12 228202
73662 4438 71487 4790 chr13 187956
60363 3940 59247 4383 chr14 153728
55349 4438 54290 4213 chr15 142904
59141 4065 56299 4282 chr16 149162
53149 4280 53703 4733 chr17 139856
55880 3403 53827 3537 chr18 138330
44108 3713 43764 4077 chr19 112003
47070 2859 48523 3230 chr20 128709
30756 1817 30593 2044 chr21 85724
28617 1876 28517 2149 chr22 86719
1914116 123461 1880838 134073 Total 4842167
Apple M2 .zsh:
#!/bin/zsh
# compare my WGS .vcf files with denisovan & neanderthal
# print only GRCh38 location, based on chr1, ... chr22
# Are any found in YSEQ, Sequencing or Nebula Genomics .vcf
# /Users/Wtyiii/Desktop/2024/vcf/SQFD7247.snp-indel.genome.vcf
# /Users/Wtyiii/Desktop/2024/vcf/NBU3T732.vcf
# /Users/Wtyiii/Desktop/2024/vcf/13772_hg38.vcf
# /Users/Wtyiii/Desktop/2024/vcf/37987_hg38.vcf
#for i in {22..22} ;do
#for i in {21..10} ;do
for i in {9..1} ;do
date
# My chr.., location is $2
awk -v a="chr"$i '{if($1==a)print $2;}' /Users/Wtyiii/Desktop/2024/vcf/NBU3T732.vcf > x
wc x
# 86719 86719 780471 x
sort -n x > xS
# Nebula Genomics should only list changes for me
awk -v a="chr"$i '{if($1==last)j++;last=$1;k++;}END{printf("repeat %d of %d in %s\n",j,k,a);}' xS
#repeat 0 of 86719 in chr0
cp x y
# other chr..
cat denisovan/chr$i.vcf >> y
sort -n y > yS
awk -v a="chr"$i '{if($1==last)j++;last=$1;k++;}END{printf("repeat %d of %d in %s\n",j,k,a);}' yS
# if in both, print to a (my WGS) & b
awk '{if($1==last)print $0;last=$1;}' yS > both
wc both
# 28617 28617 257553 both
awk -v a="chr"$i '{if($1==a)printf("%s\t%s\t%s\n",$2,$4,$5);}' /Users/Wtyiii/Desktop/2024/vcf/NBU3T732.vcf > xx
awk 'NR==FNR {h[j]=$1;j++;next}{if($1==h[k]){printf("%s\n",$0);k++;}}' both xx > c
wc c
gunzip -ck denisovan.hg38.filt.vcf.gz | \
awk -v a="chr"$i '{if(a==$1){printf("%s\t%s\t%s\n",$2,$4,$5);}}' > yy
wc yy
awk 'NR==FNR {h[i]=$1;i++;next}{if($1==h[k]){printf("%s\n",$0);k++;}}' both yy > d
wc d
mv c denisovan0/c$i
mv d denisovan0/d$i
rm yy xx x xS y yS both
date
done