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Commit 1c1e036e authored by Venkat Malladi's avatar Venkat Malladi
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Fix filter reads output.

parent b47a158e
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workflow/scripts/map_qc.py
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...@@ -153,7 +153,7 @@ def dedup_mapped(bam, bam_basename, paired): ...@@ -153,7 +153,7 @@ def dedup_mapped(bam, bam_basename, paired):
'''Use sambamba and samtools to remove duplicates.''' '''Use sambamba and samtools to remove duplicates.'''
# Markduplicates # Markduplicates
dup_file_qc_filename = bam_basename + ".dup.qc" dup_file_qc_filename = bam_basename + ".dedup.qc"
tmp_dup_mark_filename = bam_basename + ".dupmark.bam" tmp_dup_mark_filename = bam_basename + ".dupmark.bam"
sambamba_params = "--hash-table-size=17592186044416" + \ sambamba_params = "--hash-table-size=17592186044416" + \
" --overflow-list-size=20000000 --io-buffer-size=256" " --overflow-list-size=20000000 --io-buffer-size=256"
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