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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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ask about the “AD.hIGH" NOT FOUND #32

Open lnqiao opened 4 years ago

bmansfeld commented 4 years ago

Sorry please try to better state the issue and bug. I hope I can help you

lnqiao commented 4 years ago

when I conduct the inport form gatk, it was failed and said that "> df <-

lnqiao commented 4 years ago

when I conduct the inport form gatk, it was failed and said that "> df <-

lnqiao commented 4 years ago

I already put the code and warnings together.

lnqiao 邮箱：lnqiao@cau.edu.cn

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On 06/11/2020 22:57, Ben Mansfeld wrote:

Sorry please try to better state the issue and bug. I hope I can help you

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

bmansfeld commented 4 years ago

Thanks. Please supply the head of your table file as well as the commands you used prior to importFromGATK This will help me understand why the import function is unable to parse your data correctly and identify the column names. Ben

lnqiao commented 4 years ago

the whole code are as fllows library("QTLseqr")

Set sample and file names

Mut <- "W" WT <- "G"

file <- "combine1.reform.table"

df <- importFromGATK( file = file, highBulk = Mut, lowBulk = WT,

chr=c('chr01')zmf88982123

)

Filter SNPs based on some criteria

and the head of input file are as follows：

CHROM POS REF ALT G.AD G.DP G.GQ G.PL W.AD W.DP W.GQ W.PL chr01 19597 T G 27, 16 43 99 493, 0, 1022 20, 22 42 99 418, 0, 449 chr01 21391 C T 5, 10 15 99 405, 0, 180 16, 6 22 99 204, 0, 602 chr01 26239 T C 12, 10 22 99 308, 0, 401 18, 20 38 99 419, 0, 331 chr01 26300 G A 11, 12 23 99 400, 0, 356 26, 22 48 99 419, 0, 540 chr01 26899 T C 15, 7 22 99 194, 0, 525 10, 16 26 99 338, 0, 180 chr01 80750 A G 9, 13 22 99 413, 0, 311 14, 20 34 99 393, 0, 244 chr01 114667 T C 0, 4 4 69 162, 0, 69 10, 8 18 99 288, 0, 748 chr01 124990 T A 17, 9 26 99 298, 0, 632 14, 14 28 99 262, 0, 281 chr01 188659 C G 11, 7 18 99 261, 0, 371 20, 14 34 99 487, 0, 393

Thankful for your kindly instruction：

Nanqiao Liao Zhejiang University,China

At 2020-06-12 00:02:15, "Ben Mansfeld" notifications@github.com wrote:

Thanks. Please supply the head of your table file as well as the commands you used prior to importFromGATK This will help me understand why the import function is unable to parse your data correctly and identify the column names. Ben

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

bmansfeld commented 4 years ago

Nanqiao, I figured out what the issue is. As I suspected the problem is with the names of your columns "W" and "G". It is an end case in the column renaming step I perform after importing. I can make a fix for this soon but it's not my top priority at the moment. The good news is that if you change the column names to longer more informative names even to "Mut" and "WT" in the actual table file. This will make it work for you in the mean time and you can continue the analysis. Good luck, Ben