plink --extract参数采坑问题记录

plink --extract采坑问题记录

问题描述：使用–extract 参数后没能正常进行LD修剪

~/software/miniconda2/bin/plink --cow --allow-extra-chr -noweb --file /home/yanglv/soft_project/Target/target_result_test/result_5_3_clean_dropna2_filter_19sample/admixture_pairwise_50_10_0_2/test/admixture_pairwise_50_10_0_2 --geno 0.1 --make-bed --indep-pairwise 50 10 0.1

# 322 variants removed due to missing genotype data (--geno).
# 70918 variants and 581 cattle pass filters and QC.
# Pruning complete.  47613 of 70918 variants removed.
# Marker lists written to
# /home/yanglv/soft_project/Target/target_result_test/result_5_3_clean_dropna2_filter_19sample/admixture_pairwise_50_10_0_2/test1_admixture.prune.in
# and
# /home/yanglv/soft_project/Target/target_result_test/result_5_3_clean_dropna2_filter_19sample/admixture_pairwise_50_10_0_2/test1_admixture.prune.out

~/software/miniconda2/bin/plink --cow --allow-extra-chr -noweb --bfile plink --extract plink.prune.in --make-bed --out pruned_test1_admixture

Note: --noweb has no effect since no web check is implemented yet.
514998 MB RAM detected; reserving 257499 MB for main workspace.
Allocated 193124 MB successfully, after larger attempt(s) failed.
70918 variants loaded from .bim file.
581 cattle (0 males, 0 females, 581 ambiguous) loaded from .fam.
Ambiguous sex IDs written to pruned_test1_admixture.nosex .
--extract: 23836 variants remaining.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 581 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.967899.
23836 variants and 581 cattle pass filters and QC.
Note: No phenotypes present.
--make-bed to pruned_test1_admixture.bed + pruned_test1_admixture.bim +
pruned_test1_admixture.fam ... done.

出现警告，大事不妙。
果然，惊奇的发现提取后的文件居然和原文件一模一样，即第二句完全没有起到作用。
猜测是我的map文件中SNP名称全用.来表示导致的。

1	.	0	100223803
1	.	0	100875122
1	.	0	102759472
1	.	0	102948333
1	.	0	103269622
1	.	0	106304192
1	.	0	109386355
1	.	0	112881004

随即修改第二列进行测试：第二列为SNP名称，需要与其他名称不同。整合第一列和第四列作为名称

1	1_100223803	0	100223803
1	1_100875122	0	100875122
1	1_102759472	0	102759472
1	1_102948333	0	102948333
1	1_103269622	0	103269622
1	1_106304192	0	106304192
1	1_109386355	0	109386355
1	1_112881004	0	112881004