Samtools is designed to work on a stream. It regards an input file-' as the standard input (stdin) and an output file-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error output (...
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Samtools is designed to work on a stream. It regards an input file `-' as the standard input (stdin) and an output file `-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error ou...
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am having a similar issue when trying to perform bcftools merge. I get these errors with the first file in the list,[E::hts_hopen] Failed to open file filename.bcf.csiand[E::hts_open_format] Failed to open file filename.bcf.csiandFailed to open filename.bcf.csi Exec format error....
{REF_GENOME} \ --annotate FORMAT/AD,FORMAT/DP,INFO/AD \ --max-depth 100000 \ --max-idepth 100000 \ ${SC_BAM} | \ ${BCFTOOLS_EXEC} call \ --keep-alts \ -C alleles \ -T ${CANDIDATE_ALLELE} \ --multiallelic-caller \ -Ou | \ ${BCFTOOLS_EXEC} norm \ -Oz \ -o ${SC_...
[i]\n" " exec('def xfit(x): return '+pfit[5])\n" " istart = int(pfit[3])\n" " iend = int(pfit[4])+1\n" " vals = dat[chr][istart:iend]\n" " args = {}\n" " if i==0: args = {'label':'Target to Fit'}\n" " ax.plot([x[2] for x in vals],[x[3...
(*str); str++; } } static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { #if ENABLE_PERL_FILTERS PerlInterpreter *perl = flt->perl; if ( !perl ) error("Error: perl expression without a perl script name\n"); dSP; ENTER; SAVE...