2025-01-13 20:24:20 +08:00
|
|
|
thread=128
|
|
|
|
|
|
|
|
|
|
n1=~/data/na12878-1.fq.gz
|
|
|
|
|
n2=~/data/na12878-2.fq.gz
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D1/1w1.fq
|
|
|
|
|
#n2=~/data/dataset/real/D1/1w2.fq
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D1/n1.fq.gz
|
|
|
|
|
#n2=~/data/dataset/real/D1/n2.fq.gz
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D2/n1.fq.gz
|
|
|
|
|
#n2=~/data/dataset/real/D2/n2.fq.gz
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D3/n1.fq.gz
|
|
|
|
|
#n2=~/data/dataset/real/D3/n2.fq.gz
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D4/n1.fq.gz
|
|
|
|
|
#n2=~/data/dataset/real/D4/n2.fq.gz
|
|
|
|
|
|
|
|
|
|
#n1=~/data/dataset/real/D5/n1.fq.gz
|
|
|
|
|
#n2=~/data/dataset/real/D5/n2.fq.gz
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
reference=~/data/fmt_ref/human_g1k_v37_decoy.fasta
|
|
|
|
|
|
|
|
|
|
out=./out.sam
|
2024-06-24 18:11:54 +08:00
|
|
|
#out=/dev/null
|
2025-01-13 20:24:20 +08:00
|
|
|
sudo /home/zzh/clean_mem.sh
|
|
|
|
|
rm $out
|
2023-12-25 11:11:19 +08:00
|
|
|
|
2024-04-06 20:53:42 +08:00
|
|
|
time ./fastbwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
|
2024-08-06 03:08:10 +08:00
|
|
|
$reference \
|
2025-01-13 20:24:20 +08:00
|
|
|
$n1 \
|
|
|
|
|
$n2 \
|
|
|
|
|
-o $out -2 #-Z
|
|
|
|
|
|
|
|
|
|
#-K 2560000000 \
|
|
|
|
|
#-K 2100000000
|
