/rhome/jmarz001/shared/SEQ_RUNS/10_8_2018/FASTQ/

UCRKL000010 CCV Davis F25
10_S226_L003_R1_001.fastq.gz
10_S226_L003_R2_001.fastq.gz
10_S226_L004_R1_001.fastq.gz
10_S226_L004_R2_001.fastq.gz

UCRKL000016 CCV Davis F42
16_S227_L003_R1_001.fastq.gz
16_S227_L003_R2_001.fastq.gz
16_S227_L004_R1_001.fastq.gz
16_S227_L004_R2_001.fastq.gz

UCRKL000024 CCXXI Davis F25
24_S228_L003_R1_001.fastq.gz
24_S228_L003_R2_001.fastq.gz
24_S228_L004_R1_001.fastq.gz
24_S228_L004_R2_001.fastq.gz

UCRKL000250 CCII Boz F27
250_S229_L003_R1_001.fastq.gz
250_S229_L003_R2_001.fastq.gz
250_S229_L004_R1_001.fastq.gz
250_S229_L004_R2_001.fastq.gz

UCRKL000255 CCII Boz F50
255_S230_L003_R1_001.fastq.gz
255_S230_L003_R2_001.fastq.gz
255_S230_L004_R1_001.fastq.gz
255_S230_L004_R2_001.fastq.gz

UCRKL000257 CCV Davis F6
257_S231_L003_R1_001.fastq.gz
257_S231_L003_R2_001.fastq.gz
257_S231_L004_R1_001.fastq.gz
257_S231_L004_R2_001.fastq.gz

UCRKL000258 CCV Boz F6
258_S232_L003_R1_001.fastq.gz
258_S232_L003_R2_001.fastq.gz
258_S232_L004_R1_001.fastq.gz
258_S232_L004_R2_001.fastq.gz

UCRKL000262 CCV Boz F25
262_S233_L003_R1_001.fastq.gz
262_S233_L003_R2_001.fastq.gz
262_S233_L004_R1_001.fastq.gz
262_S233_L004_R2_001.fastq.gz

UCRKL000267 CCXXI Davis F11
267_S234_L003_R1_001.fastq.gz
267_S234_L003_R2_001.fastq.gz
267_S234_L004_R1_001.fastq.gz
267_S234_L004_R2_001.fastq.gz

attempt to split the fastq files by barcode, uncertain if it works

move the files from their SEQ_RUN storage into the project data directory and unzip them

count the number of reads in each unzipped fastq file
in future, would like to add lines to add reads together per population and per sequencing lane (for now done manually)

generate fastqc (quality) data from the raw fastq files, store them in the fastqc directory

unzips the fastq-fastqc files so the files are put in a directory and you can access the quality, etc.

trim the reads based on length, quality, sliding window &etc.

count the number of reads in each trimmed file
in future, should add code to print retained reads (print reads in trimmed files, intake fq.seq.sh reads, and divide to produce percent retained reads)

generate fastqc data from trimmed fastq files, stored in subdirectory of fastqc dir

align to chromosome split whole genome fasta and assign read groups based on population and lane
sort bams and make unmapped files, etc

mark duplicates in the bam files

call snps with freebayes with split genome sections indicated for speed,
feed in all files so that snp calls are more accurate, output one vcf file
population info can still be used because of read group labels

filter called snps based on:
quality distribution, missing data distribution, % homozygous and heterozygous, depth & heterozygosity, minor allele frequency, allele balance, allele observations, and haplotype variant calls according to proximity