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I had e.g. errors like this
[duphold] couldn't find sample:sqcudn971184 in snps vcf which had:sqcudn971184.187147
due to bam file and snps VCF file differing in sample names(in bams the names are truncated). Previously, have solved this issue with renaming the header of the snp VCF(removing the .187147). However this time tried to set up like this export DUPHOLD_SAMPLE_NAME='sqcudn971184' or just this DUPHOLD_SAMPLE_NAME='sqcudn971184' which doesn't work.
I would appreciate any leads on this.
The text was updated successfully, but these errors were encountered:
Hello @brentp,
Thank you for this tool!
I had e.g. errors like this
[duphold] couldn't find sample:sqcudn971184 in snps vcf which had:sqcudn971184.187147
due to bam file and snps VCF file differing in sample names(in bams the names are truncated). Previously, have solved this issue with renaming the header of the snp VCF(removing the .187147). However this time tried to set up like this
export DUPHOLD_SAMPLE_NAME='sqcudn971184'
or just thisDUPHOLD_SAMPLE_NAME='sqcudn971184'
which doesn't work.I would appreciate any leads on this.
The text was updated successfully, but these errors were encountered: