WebSep 6, 2024 · Samtools gives "truncated file" when trying to view a "reheaded" file. I have a BAM file that works fine, but after using samtools reheader, I cannot view it in samtools. The new file has the same size as the original. I run the command: samtools reheader -P header.sam input.bam > output.bam. WebAnyway, the quickest way to do what you want is to samtools view -H foo.bam > header to get the BAM header and then change each NCBI "chromosome name" to its corresponding UCSC chromosome name. DO NOT REORDER THE LINES! You can then use samtools reheader and be done.

samtools-reheader(1) manual page

WebAnyway, the quickest way to do what you want is to samtools view -H foo.bam > header to get the BAM header and then change each NCBI "chromosome name" to its corresponding … WebAug 19, 2024 · there is no option -sample so your command is interpreted as -s ample, however the failure was not checked there are no FORMAT fields in your VCF, therefore it makes no sense to add samples gzipped files are not supported by reheader, you'll need to convert to plain VCF, BCF, or BGZF-compressed VCF or BCF. the tail wags

samtools-reheader: replaces the header in the input file

WebThe following are 30 code examples of subprocess.call () . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module subprocess , or try the search function . Example #1 WebFor example, when performing line intersections, the desire may be to consider as identical all sites with matching positions (bcftools isec -c all), or only sites with matching variant … septic tank set truck