Hi In version 0.1.19 of bcftools view there is the setting:
-N which is defined as Skip sites where the REF field is not A/C/G/T I am currently running version 1.2 of bcftools and I realised that I still have -N set when calling bcftools call. However -N is not in the documentation any more suggesting it has been deprecated. However there is no error message associated with leaving the setting in so I am not sure is there any difference between leaving -N set or not When I run the following code it the resultant vcfs vcfwithN.vcf and vcfnoN.vcf are identical. samtools view -bq 20 -F 1796 chr21.sorted.markdups.bam | samtools mpileup -Egu -t DP,SP -d 5000 -f chr21.fa -L 5000 -F 0.05 -| bcftools call -cNvf GQ - > vcfwithN.vcf samtools view -bq 20 -F 1796 chr21.sorted.markdups.bam | samtools mpileup -Egu -t DP,SP -d 5000 -f chr21.fa -L 5000 -F 0.05 -| bcftools call -cvf GQ - > vcfnoN.vcf Can anyone shed some light on whether setting -N is likely to make any difference to the calling and if so what will that be or does -N have no effect and in 1.2 the function of -N occurs by default any way? Many thanks KR ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ******************************************************************************************************************** ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
