Post date: Aug 05, 2020 6:34:3 PM
List of commands for ANGSD: (estimating the effective number of sites)
Start run:
[u6028866@kingspeak2:alignments]$ srun -t 12:00:00 -n 8 -N 1 -A gompert-kp -p gompert-kp --pty /bin/bash
srun: job 8526943 queued and waiting for resources
Copy Pando bam files to my folder on the cluster
[u6028866@kingspeak1:Alignments_mem_mod]$ ls | grep "aln_mem_mod_\(017-S\|025-B\|025-S\|027-B\|037-B-rep\|037-B-Rp\|037-B\|039-S\|047-B\|049-S\|051-B\|051-S\|053-B\|053-S\|055-S-Rp\|055-S\|063-S\|065-B\|065-S\|069-B\|069-S\|071-B\|073-S\|075-B\|075-S\|083-S\|085-B\|085-S\|086-S\|087-B\|087-S\|091-B\|091-S\|093-B\|093-S\|095-B\|095-S\|103-B\|103-S\|105-B\|107-B\|107-S\|111-B\|113-B\|113-S\|121-B\|121-S\|123-B\|123-S\|125-B\|129-B\|129-S-rep\|129-S-Rp\|129-S\|131-S\|137-B\|139-B\|141-B\|143-S\|145-S\|147-S\|155-B\|155-S\|157-B\|157-S\|159-B\|159-S\|163-B\|163-S\|165-B\|165-S\|171-B\|171-S\|173-B\|173-S\|175-B\|175-S\|177-S\|179-B\|179-S\|181-S\|191-S\|195-B\|195-S\|203-S\|205-S\|207-S\|209-B\|211-B\|211-S\|219-S\|221-S\|223-B\|225-S\|235-B\|235-S\|237-B\|237-S\|239-B\|239-S\|247-S\|251-B\|251-S\|257-S\|259-B\|267-B\|269-S\|277-B\|277-S\)*.sorted.bam$" > /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/alignments/bam.list
for FILE in $(cat /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/alignments/bam.list) do cp ${FILE} /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/alignments/
done
Load angsd and samtools:
module load samtools angsd
Indexing the bam files:
for i in pando_only_bams/*.bam;do samtools index $i;done
Copy the genome in the folder
cp /uufs/chpc.utah.edu/common/home/gompert-group1/data/aspen/genome/Potrs01-genome.fa ./
angsd -bam bam.list -doSaf 1 -anc ../Potrs01-genome.fa -GL 1 -P 50 -minMapQ 1 -minQ 20 -out sfs_est
Infer the tree using another approach? http://chibba.pgml.uga.edu/snphylo/
angsd command lines
angsd -bam bam.list -doSaf 1 -anc ../Potrs01-genome.fa -GL 1 -P 40 -minMapQ 1 -minQ 20 -out sfs_est
/uufs/chpc.utah.edu/sys/installdir/angsd/0.930/angsd/misc/realSFS sfs_est.saf.idx -P 24 > final.sfs
/uufs/chpc.utah.edu/sys/installdir/angsd/0.930/angsd/misc/realSFS saf2theta sfs_est.saf.idx -sfs final.sfs -outname out
/uufs/chpc.utah.edu/sys/installdir/angsd/0.930/angsd/misc/thetaStat do_stat out.thetas.idx
-> Output filenames:
->"out.thetas.gz"
->"out.thetas.idx"
Dumping file: "out.thetas.idx.pestPG"
File is in: /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/alignments/pando_only_bams/out.thetas.idx.pestPG
From there:
Where is the info about the effective number of sites?