samtools fastq \
  ERR16914980.bam \
> ERR16914980.fastq

bwa aln \
  human_g1k_v37.fasta \
  ERR16914980.fastq \
> ERR16914980.sai

gzip ERR16914980.fastq

bwa samse human_g1k_v37.fasta \
  ERR16914980.sai \
  ERR16914980.fastq.gz \
> ERR16914980.sam

samtools view \
  -@ 1 \
  -b \
  -o ERR16914980.unsorted.bam \
  ERR16914980.sam


samtools sort \
  -@ 1 \
  -m 512M \
  -T ~/samtmp/ERR16914980 \
  -o ERR16914980.aligned.bam \
  ERR16914980.unsorted.bam

samtools index ERR16914980.aligned.bam

awk '{print $1"\t"$4"\t"$4}' \
sgdp_erfurt_saxon_ireland_final.bim \
> 1240K.pos

awk 'BEGIN{OFS="\t"}
{
 chr=$1
 if(chr==23) chr="X"
 print chr,$2,$3
}' 1240K.pos > 1240K_X.pos

bcftools mpileup \
  -f human_g1k_v37.fasta \
  -R 1240K_X.pos \
  ERR16914980.aligned.bam \
| bcftools call -c -Ov \
> ERR16914980.vcf

plink1.9 \
  --vcf ERR16914980.vcf \
  --make-bed \
  --out ERR16914980
  
3. FID setzen
awk 'BEGIN{OFS="\t"} {$1="Tarrega"; print}' \
ERR16914980.fam > tmp && mv tmp ERR16914980.fam

4. SNP-IDs angleichen
Wie vorher:

awk 'BEGIN{OFS="\t"}
{
 chr=$1
 if(chr==23) chr="X"
 if(chr==24) chr="Y"
 $2=chr":"$4
 print
}' ERR16914980.bim > tmp.bim

mv tmp.bim ERR16914980.bim


plink1.9 \
  --bfile ERR16914980 \
  --missing \
  --out ERR16914980_missing