README.md

In BGI-LuoWen/lwlegopt: luo wen's lego-plot tool

R packages

This tool is used to plot 3D-lego image for mutation spectrum.

Instructions

1

library(lwlegopt)

data(Mutdata)

Draw_lego(h)

2

library(lwlegopt)

Draw_lego(path="example",file_name='TCGA.originalGenomes_with_types.txt')

3

library(lwlegopt)

Draw_lego(path="example",file_name='combined_mutations.out.xls',title='CRC',prepare=TRUE,samtools='/usr/bin/samtools/samtools',fasta='/usr/Database/human_19/hg19_fasta_GATK/hg19.fasta')

data preparing

For # 3 , Inputfile which generated by MUTECT has the following format：

contig position context ref_allele alt_allele tumor_name normal_name score dbsnp_site covered power tumor_power normal_power normal_power_nsp normal_power_wsp total_reads map_Q0_reads init_t_lod t_lod_fstar t_lod_fstar_forward t_lod_fstar_reverse tumor_f contaminant_fraction contaminant_lod t_q20_count t_ref_count t_alt_count t_ref_sum t_alt_sum t_ref_max_mapq t_alt_max_mapq t_ins_count t_del_count normal_best_gt init_n_lod normal_f n_q20_count n_ref_count n_alt_count n_ref_sum n_alt_sum power_to_detect_positive_strand_artifact power_to_detect_negative_strand_artifact strand_bias_counts tumor_alt_fpir_median tumor_alt_fpir_mad tumor_alt_rpir_median tumor_alt_rpir_mad observed_in_normals_count failure_reasons judgement

chr1 17296739 CTTxTGT C T 136869-17 HZYblood 0 NOVEL COVERED 0.992926 0.992926 1 1 1 151 0 107.6196 107.6196 88.747485 32.232969 0.5 0.02 2.326076 63 31 31 1120 1115 60 60 0 0 CC 26.15388 0 85 87 0 3102 0 0.999999 1 (21,13,25,10) 52 21 37 24 0 KEEP

chr1 19969975 AAAxTTA G A 136869-17 HZYblood 0 NOVEL COVERED 0.981955 0.981955 1 1 1 155 0 92.045794 92.107961 19.248768 83.141925 0.464286 0.02 2.38739 57 30 26 1117 965 60 60 0 0 GG 29.473437 0 96 98 0 3559 0 1 0.998117 (6,25,6,23) 59 21 40 23 0 KEEP

chr1 151258755 TCTxGGA G T 136869-17 HZYblood 0 NOVEL COVERED 1 1 1 1 1 239 0 26.606803 44.195015 39.662284 9.59092 0.125 0.02 4.634466 129 112 16 4153 575 60 60 0 0 GG 32.802707 0 107 109 0 4016 0 0.985573 0.99995 (85,40,14,4) 44.5 22 54.5 22 0 KEEP

BGI-LuoWen/lwlegopt documentation built on May 5, 2019, 10:25 a.m.