القائمة
Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
| name | blast2sam-pl |
| description | Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling. |
| disable-model-invocation | true |
| user-invocable | true |
blast2sam.pl [-s] [-d] input.blast > output.sam/home/vimalinx/miniforge3/envs/bio/bin/blast2sam.plblastn text output into SAM records.samtools or other SAM/BAM-aware tooling.-s when downstream tools need SAM field 10 populated.-d when a downstream parser insists on SAM field 11.# 1) Convert legacy BLASTN text output into headerless SAM
blast2sam.pl \
alignments.blast > alignments.sam
# 2) Include aligned query sequence plus dummy qualities
blast2sam.pl \
-sd \
alignments.blast > alignments.with-seq.sam
# 3) Add a SAM header afterwards for downstream tools that require one
blast2sam.pl -sd alignments.blast > alignments.sam
samtools view -hT reference.fa alignments.sam > alignments.with-header.sam
blastn output in the default pairwise text format, not tabular or XML output.blast2sam.pl, adding -s if downstream tools need sequence and -d if they also need quality strings.blastn output; it is not the right tool for BLAST tabular, XML, JSON, or generic BLAST+ -outfmt outputs.--help works via Perl Getopt::Std, but -help is wrong here and is split into -h -e -l -p, which produces unknown-option errors.-s prints the aligned query sequence, not necessarily the original full read sequence from FASTQ input.-d fills SAM field 11 with dummy I characters (Phred 40 style); use that only when fake quality scores are acceptable.