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Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling.
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Based on SOC occupation classification
| 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.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.