---
title: "15-angsd"
author: "Steven Roberts"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
editor_options: 
  markdown: 
    wrap: sentence
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
library(pheatmap)
library(DESeq2)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```
```{bash}
/home/shared/ngsTools/angsd/angsd --help
```
```{bash}
cd ../output/14-BWA
ls *.bam | awk '{print "../output/14-BWA/" $0}' > ../15-angsd/bamlist.txt
```

```{bash}
samtools faidx ../data/GCF_031168955.1_ASM3116895v1_genomic.fna
```


```{bash}
/home/shared/ngsTools/angsd/angsd | head -n 1
```


```{bash}
/home/shared/ngsTools/angsd/angsd \
  -b ../output/15-angsd/bamlist.txt \
  -ref ../data/GCF_031168955.1_ASM3116895v1_genomic.fna \
  -out ../output/15-angsd/gmac_01 \
  -doSaf 1 \
  -fold 1 \
  -GL 1 \
  -doMajorMinor 1 \
  -doMaf 1 \
  -minMapQ 30 \
  -minQ 20 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1
```
```{bash}
/home/shared/ngsTools/angsd/angsd \
  -b ../output/15-angsd/bamlist.txt \
  -ref ../data/GCF_031168955.1_ASM3116895v1_genomic.fna \
  -out ../output/15-angsd/gmac_01 \
  -doSaf 1 \
  -fold 1 \
  -GL 1 \
  -doMajorMinor 1 \
  -doMaf 1 \
  -minMapQ 30 \
  -minQ 20 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1 \
  -anc ../data/GCF_031168955.1_ASM3116895v1_genomic.fna
```
 Step 1: Calculate genotype likelihoods & SFS likelihoods


```{bash}
/home/shared/angsd0.940/angsd \
  -b ../output/15-angsd/bamlist.txt \
  -ref ../data/GCF_031168955.1_ASM3116895v1_genomic.fna \
  -out ../output/15-angsd/gmac_02 \
  -doSaf 1 \
  -GL 1 \
  -doMajorMinor 1 \
  -doMaf 1 \
  -minMapQ 30 \
  -minQ 20 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1
```

🧬 Step 2: Estimate the folded SFS from SAF index

```{bash}
/home/shared/angsd0.940/realSFS ../output/15-angsd/gmac_02.saf.idx > ../output/15-angsd/gmac_02.sfs
```