Hello dears all,
Actually I have a vcf file which it has been generated through samtools/bcftools pipeline. This file doesn't have just the sample names, indeed it has the samples' PATH in it. So what I want to do is removing the PATH and simply just keep the sample names. Moreover, if it is possible to remove these PATH from a.ped file I would be grateful if you can help me to solve my error. Here is a part of my vcf and as it can be seen there is PATH for each sample:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /home2/omid/alignment/BAM/F0-F06-10-markdup.bam /home2/omid/alignment/BAM/F0-F06-11-markdup.bam /home2/omid/alignment/BAM/F0-F06-12-markdup.bam /home2/omid/alignment/BAM/F0-F06-13-markdup.bam /home2/omid/alignment/BAM/F0-F07-11-markdup.bam /home2/omid/alignment/BAM/F0-F07-12-markdup.bam /home2/omid/alignment/BAM/F0-F07-13-markdup.bam /home2/omid/alignment/BAM/F0-F07-14-markdup.bam /home2/omid/alignment/BAM/F0-F08-11-markdup.bam /home2/omid/alignment/BAM/F0-F08-12-markdup.bam /home2/omid/alignment/BAM/F0-F25-10-markdup.bam /home2/omid/alignment/BAM/F0-F25-11-markdup.bam /home2/omid/alignment/BAM/F0-F25-12-markdup.bam /home2/omid/alignment/BAM/F0-F25-13-markdup.bam /home2/omid/alignment/BAM/F0-F25-14-markdup.bam /home2/omid/alignment/BAM/F0-F25-15-markdup.bam /home2/omid/alignment/BAM/F0-F25-16-markdup.bam
Thank you very much in advance.
Regards,
Omid
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jaafari.omid
Take a look at bcftools reheader, which should be able to solve your issue.
Thank you for your answer. I will give it a try and hope it work.
Cheers,
Omid
Thank you very much. It worked properly.
Regards,
Omid
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Change sample names in vcf
Thank you so much, I will check it.
regards,
Omid