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Activity overviewLatest activity by cali
Hi Genevieve Brandt (she/her) The BAMs were aligned with BWA-mem v 0.7.17, sorted and indexed (CSI) with SAMtools v 1.10, BAMs merged to per-sample BAM with SAMbamba v 0.7.1, duplicate reads marke...
Hi Genevieve Brandt (she/her) ValidateSamFile in summary mode shows the following: Error Type CountERROR:INVALID_INSERT_SIZE 134030WARNING:REF_SEQ_TOO_LONG_FOR_BAI 1 And with "IGNORE_WARNINGS" and ...
Hi Genevieve Brandt (she/her) Thanks for your reply. Only the header differs: $ sdiff -s bam_headers.txt dict_first3cols.txt @HD VN:1.3 SO:coordinate | @HD VN:1.4 SO:unsorted I would be surprised i...
cali created a post,
ApplyBQSR to unmapped reads for non-model organism does not work with '-L unmapped' flag
GATK version used: 22.214.171.124 and 126.96.36.199 Exact command used: This does NOT work: bam_in=whole_genome_sorted.bamgatk ApplyBQSR --java-options "-Xmx4G -Dsamjdk.compression_level=5 -DGATK_STACKTRACE...
gatk ApplyBQSR \--java-options "-Xmx6G -Dsamjdk.compression_level=5" \-R $ref \-I $bam_in \--bqsr-recal-file $table \-L $contig \-O $bam_out