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When you encounter an core dumped error while using the plink1.9 version, run the command as follows:

/ share/work/biosoft/plink/plink_v1.9/plink-vcf / share/nas1/wangq/project/pop_test/pop_cucu_demo/work/ann/1.qc_filter/filtered_snp.vcf.gz-- make-bed-- extract ld.prune.in-- out LDfiltered-- recode vcf-iid-- keep-allele-order-- allow-extra-chr-- set-missing-var-ids @:

The error message is as follows:

PLINK v1.90b3.32 64-bit (24 Feb 2016) https://www.cog-genomics.org/plink2(C) 2005-2016 Shaun Purcell Christopher Chang GNU General Public License v3Logging to LDfiltered.log.Options in effect:-allow-extra-chr-- extract ld.prune.in-- keep-allele-order-- make-bed-- out LDfiltered-- recode vcf-iid-- set-missing-var-ids @: #-- vcf / share/nas1/wangq/project/pop_test/pop_cucu_demo/work/ann/1.qc_filter/filtered_snp.vcf.gz128701 MB RAM detected Reserving 64350 MB for main workspace.--vcf: LDfiltered-temporary.bed + LDfiltered-temporary.bim + LDfiltered-temporary.fam written.9696 variants loaded from .bim file.9696 missing IDs set.114 people (0 males, 0 females, 114 ambiguous) loaded from .fam.ambiguous sex IDs written to LDfiltered.nosex.-- extract: 435 variants remaining.Using 1 thread (no multithreaded calculations invoked.Before main variant filters, 114 founders and 0 nonfounders present.Calculating allele frequencies...) Done.Total genotyping rate is 0.952531.435 variants and 114people pass filters and QC.Note: No phenotypes present.--make-bed to LDfiltered.bed + LDfiltered.bim + LDfiltered.fam. Done.--recode vcf-iid to LDfiltered.vcf... Done.Segmentation fault (core dumped)

After trying various methods and using version 2.0 plink, I did not encounter this error again.

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