Cant read baf file

[gonzaparra]

Hi,

I am trying to read the baf file that was generated using BAFExtract.

loh <- readBAFExtractOutput ( path="/dir/CASPER/result", sequencing.type="single-cell")

I get the following error: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/dir/CASPER/result/NA': No such file or directory

This is the list of files that are present in that folder: 10_allele_counts.bin 1_allele_counts.bin 6_mcf_hap5_allele_counts.bin Un_gl000216_allele_counts.bin Un_gl000235_allele_counts.bin 11_allele_counts.bin 1_gl000191_random_allele_counts.bin 6_qbl_hap6_allele_counts.bin Un_gl000217_allele_counts.bin Un_gl000236_allele_counts.bin 11_gl000202_random_allele_counts.bin 1_gl000192_random_allele_counts.bin 6_ssto_hap7_allele_counts.bin Un_gl000218_allele_counts.bin Un_gl000237_allele_counts.bin 12_allele_counts.bin 20_allele_counts.bin 7_allele_counts.bin Un_gl000219_allele_counts.bin Un_gl000238_allele_counts.bin 13_allele_counts.bin 21_allele_counts.bin 7_gl000195_random_allele_counts.bin Un_gl000220_allele_counts.bin Un_gl000239_allele_counts.bin 14_allele_counts.bin 21_gl000210_random_allele_counts.bin 8_allele_counts.bin Un_gl000221_allele_counts.bin Un_gl000240_allele_counts.bin 15_allele_counts.bin 22_allele_counts.bin 8_gl000196_random_allele_counts.bin Un_gl000222_allele_counts.bin Un_gl000241_allele_counts.bin 16_allele_counts.bin 2_allele_counts.bin 8_gl000197_random_allele_counts.bin Un_gl000223_allele_counts.bin Un_gl000242_allele_counts.bin 17_allele_counts.bin 3_allele_counts.bin 9_allele_counts.bin Un_gl000224_allele_counts.bin Un_gl000243_allele_counts.bin 17_ctg5_hap1_allele_counts.bin 4_allele_counts.bin 9_gl000198_random_allele_counts.bin Un_gl000225_allele_counts.bin Un_gl000244_allele_counts.bin 17_gl000203_random_allele_counts.bin 4_ctg9_hap1_allele_counts.bin 9_gl000199_random_allele_counts.bin Un_gl000226_allele_counts.bin Un_gl000245_allele_counts.bin 17_gl000204_random_allele_counts.bin 4_gl000193_random_allele_counts.bin 9_gl000200_random_allele_counts.bin Un_gl000227_allele_counts.bin Un_gl000246_allele_counts.bin 17_gl000205_random_allele_counts.bin 4_gl000194_random_allele_counts.bin 9_gl000201_random_allele_counts.bin Un_gl000228_allele_counts.bin Un_gl000247_allele_counts.bin 17_gl000206_random_allele_counts.bin 5_allele_counts.bin M_allele_counts.bin Un_gl000229_allele_counts.bin Un_gl000248_allele_counts.bin 18_allele_counts.bin 6_allele_counts.bin Un_gl000211_allele_counts.bin Un_gl000230_allele_counts.bin Un_gl000249_allele_counts.bin 18_gl000207_random_allele_counts.bin 6_apd_hap1_allele_counts.bin Un_gl000212_allele_counts.bin Un_gl000231_allele_counts.bin X_allele_counts.bin 19_allele_counts.bin 6_cox_hap2_allele_counts.bin Un_gl000213_allele_counts.bin Un_gl000232_allele_counts.bin Y_allele_counts.bin 19_gl000208_random_allele_counts.bin 6_dbb_hap3_allele_counts.bin Un_gl000214_allele_counts.bin Un_gl000233_allele_counts.bin result.baf 19_gl000209_random_allele_counts.bin 6_mann_hap4_allele_counts.bin Un_gl000215_allele_counts.bin Un_gl000234_allele_counts.bin

Thanks in advance

[gonzaparra]

I guess the problem is related to my folder not containing files with "snp" suffix, which is the value by default for that function. I changed it to baf, is that correct to do?

Should I have snp files in that folder?

Thanks

Gonzalo

[akdess]

Dear Gonzalo, Thanks a lot for your interest! You should change the suffix to “.baf”. Sorry for the confusion. I will update the tutorials.