---
title: "20-BS-snper"
output: html_document
---

```{bash}
cd /home/shared/8TB_HDD_01/sr320/github/ceabigr/data/big
wget -r \
--no-check-certificate \
--quiet \
--no-directories --no-parent \
-P . \
-A *sorted.bam \
https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/120321-cvBS/
```

```{bash}
cd ../data

    perl /home/shared/BS-Snper-master/BS-Snper.pl \
    big/3F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam \
    --fa Cvirginica_v300.fa \
    --output ../output/20-BS-Snper/SNP-candidates.txt \
    --methcg ../output/20-BS-Snper/CpG-meth-info.tab \
    --methchg ../output/20-BS-Snper/CHG-meth-info.tab \
    --methchh ../output/20-BS-Snper/CHH-meth-info.tab \
    > ../output/20-BS-Snper/SNP.out 2> ../output/20-BS-Snper/ERR.log
```

```{bash}
tail ../output/20-BS-Snper/SNP.out
```


