Name		Name	Last commit message	Last commit date
Latest commit History 204 Commits
RNAseq		RNAseq
1liners.md		1liners.md
LICENSE		LICENSE
README.md		README.md
assignScafNumbersVCF.py		assignScafNumbersVCF.py
bam_sort_index.sh		bam_sort_index.sh
bwa.sh		bwa.sh
bwa_mem.sh		bwa_mem.sh
bwa_samse.sh		bwa_samse.sh
clean_runInfo.py		clean_runInfo.py
clean_runInfo.sh		clean_runInfo.sh
clean_up_fasta_header.py		clean_up_fasta_header.py
cluste.r		cluste.r
correct_long_name.py		correct_long_name.py
dropCloseVars.py		dropCloseVars.py
dropHighCovVars.py		dropHighCovVars.py
estpEM		estpEM
exclude_short_seqs.py		exclude_short_seqs.py
exclude_short_seqs.sh		exclude_short_seqs.sh
extract_short_long_from_fa.py		extract_short_long_from_fa.py
extract_short_long_from_fa_no_underscores.py		extract_short_long_from_fa_no_underscores.py
fq2fa.sh		fq2fa.sh
freq2treemix.py		freq2treemix.py
freqId2freq.py		freqId2freq.py
getDxy.py		getDxy.py
getFastaScaffoldsFromList.py		getFastaScaffoldsFromList.py
getGprobs_hetero.py		getGprobs_hetero.py
get_allele_freq_vcf.py		get_allele_freq_vcf.py
get_bam_depth.sh		get_bam_depth.sh
get_cluster_n_of_seqs.py		get_cluster_n_of_seqs.py
get_codingSeq_bool_perSNV.py		get_codingSeq_bool_perSNV.py
get_cov_per_ind.py		get_cov_per_ind.py
get_gene_length_from_gff3.py		get_gene_length_from_gff3.py
get_n_of_reads_per_ind.py		get_n_of_reads_per_ind.py
get_num_snvs_per_scaf.py		get_num_snvs_per_scaf.py
get_seq_length.py		get_seq_length.py
get_struct_q.py		get_struct_q.py
get_tophat_align_summary.py		get_tophat_align_summary.py
get_tophat_align_summary.sh		get_tophat_align_summary.sh
get_unlnkd_snp_list.py		get_unlnkd_snp_list.py
gl2genestDip.pl		gl2genestDip.pl
gl2genestDip.py		gl2genestDip.py
gl2genestDip_NA.pl		gl2genestDip_NA.pl
gl2genestTrip.pl		gl2genestTrip.pl
mafFisfltr.py		mafFisfltr.py
mafFltr.py		mafFltr.py
mpileup.sh		mpileup.sh
parse_barcodes768.pl		parse_barcodes768.pl
remove_clusters_threshold.py		remove_clusters_threshold.py
remove_collapsed_clusters.py		remove_collapsed_clusters.py
remove_long_name.py		remove_long_name.py
sam2bam.sh		sam2bam.sh
samtools_indx		samtools_indx
samtools_sort		samtools_sort
seqtk.sh		seqtk.sh
sortVcfByPop.py		sortVcfByPop.py
splitFastq_ms.pl		splitFastq_ms.pl
splitPops.py		splitPops.py
struct.sh		struct.sh
subVCFbyChrom.py		subVCFbyChrom.py
subVCFbyChromList.py		subVCFbyChromList.py
sub_gl.py		sub_gl.py
sub_vcf.py		sub_vcf.py
sub_vcf_by_snv.py		sub_vcf_by_snv.py
tophat.sh		tophat.sh
vcf2estPloidy.py		vcf2estPloidy.py
vcf2gl.pl		vcf2gl.pl
vcf2gl.py		vcf2gl.py
vcf2glTrip.pl		vcf2glTrip.pl
vcf2gt.py		vcf2gt.py
vcf2nex.py		vcf2nex.py
vcf2nex012.py		vcf2nex012.py
vcf2treemix.py		vcf2treemix.py
vcfFilter.py		vcfFilter.py
vcfFilter_fracData.py		vcfFilter_fracData.py
vsearch.sh		vsearch.sh

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