broadinstitute/picard

Issues

• Can CollectWgsMetrics fall back to slow algorithm gracefully if the fast one fails with the default read length?

  #1970 opened 4 months ago by gokalpcelik
  8

• `--USE_END_IN_UNPAIRED_READS` and `--USE_UNPAIRED_CLIPPED_END` options for `picard MarkDuplicates` have no effect

  #1959 opened 7 months ago by ChrisHIV
  12

• Error ValidateVariants -no Support for VCFv4.4

  #1978 opened a month ago by desmodus1984
  2

• Lost output/information during RenameSampleInVcf

  #1966 opened 4 months ago by desmodus1984
  12

• CollectHsMetrics AT_DROPOUT

  #1973 opened 3 months ago by jcharlton67
  1

• `FOLD_80_BASE_PENALTY` Metric from `TargetMetricsCollector` does not exclude 0 coverage regions.

  #1971 opened 4 months ago by Patrick-Schlaeger-Broad
  0

• ValidateSamFile wrong NM tag computation

  #1963 opened 6 months ago by albertocasagrande
  3

• MarkDuplicates with single end data does not write the full report

  #1944 opened 9 months ago by mattsoup
  3

• CollectWgsMetrics error, out of bound of the index?

  #1964 opened 5 months ago by juanboja
  8

• MarkDuplicates SAM validation error

  #1961 opened 5 months ago by vivekbibs
  6

• Optical duplicates

  #1962 opened 6 months ago by Nitin123-4
  4

• genotypeConcordance irregular behavior in counting after applying filters

  #1943 opened 6 months ago by Dahn-YoungDong
  3

• Running picard in parallel issue

  #1958 opened 7 months ago by Davood-Norouzi
  3

• Edge case in LiftoverVcf causes cryptic string exception

  #1951 opened 7 months ago by rickymagner
  8

• CollectHsMetrics returns negative percentages on PacBio data

  #1924 opened 7 months ago by valeandri
  5

• Issue Running Picard MarkDuplicates: File Compression Error with Snappy

  #1953 opened 7 months ago by VPatel294
  1

• UnMarkDuplicate

  #1957 opened 7 months ago by Davood-Norouzi
  1

• about MarkDuplicates

  #1954 opened 7 months ago by cnxiaobo94
  1

• java environment not detected when using option OUTPUT in BuilBamIndex

  #1947 opened 7 months ago by r-poloni
  1

• TAGGING_POLICY=OpticalOnly tags everything

  #1952 opened 7 months ago by Davood-Norouzi
  4

• How to control the number of threads

  #1950 opened 8 months ago by yitengfei120011
  1

• Picard Build Failure

  #1946 opened 8 months ago by n-belle
  6

• StringIndexOutOfBoundsException at LiftoverVcf

  #1933 opened 8 months ago by C37H41N2O6
  3

• BedToIntervalList reportedly does not handle stdin properly

  #1890 opened 8 months ago by droazen
  2

• Getting Segfault when running ReorderSam via GATK

  #1948 opened 9 months ago by rickymagner
  1

• java.lang.NegativeArraySizeException

  #1941 opened 9 months ago by pk-zhu
  2

• Conda installer

  #1897 opened a year ago by lappazos
  8

• picard MarkDuplicates error: Value was put into PairInfoMap more than once

  #1923 opened 10 months ago by RSchley
  2

• Problem with Picard tool for Collecting RNASeqMetrics

  #1926 opened 10 months ago by annepureddy
  4

• Error: A JNI error has occurred, please check your installation and try again

  #1935 opened 10 months ago by Portulaca666
  1

• MarkDuplicates: Instead of adding the read group of a read to the key, picard always adds "RG"

  #1936 opened 10 months ago by michaelgatzen
  0

• Streaming from requester-pays buckets for CrosscheckFingerprints doesn't work in Terra

  #1927 opened a year ago by rickymagner
  2

• BedToIntervalList doesn't handle empty bed region edge cases properly

  #1914 opened a year ago by rickymagner
  8

• warning: unable to load libgkl_compression.so from native/libgkl_compression.so (permission denied)

  #1916 opened a year ago by Ming-Yu615
  0

• java.io.FileNotFoundException: /tmp/CSPI.tmp15948393444880722616/7573.tmp (Too many open files)

  #1915 opened a year ago by poojancf
  1

• Inconsistencies in Picard MarkDuplicates Histogram Data Output

  #1893 opened a year ago by eric-holt
  2

• unable to run picard

  #1911 opened a year ago by shanmugavadivelps
  2

• Question marks in output of Picard tools

  #1906 opened a year ago by Yu-jinKim
  5

• INVALID_ALIGNMENT_START

  #1912 opened a year ago by miderxi
  4

• Mark Duplicates - Not Enough Fields Exception

  #1879 opened a year ago by tanyasarkjain
  2

• picard markduplicate issue

  #1894 opened a year ago by Subhajeet1997
  2

• Samtofastq does not retain all the information

  #1881 opened a year ago by ajeyab22
  5

• PICARD termination ,

  #1888 opened a year ago by Soumyadutta-basak
  2

• Installation problem of v3.1.0

  #1905 opened a year ago by FionaMoon
  4

• --TMP_DIR parameter is ignored and tmp dir defaults to /tmp for CollectInsertSizeMetrics (and possibly more picard tools))

  #1907 opened a year ago by gokalpcelik
  1

• Creating

  #1899 opened a year ago by kibanez
  1

• Guide to Installing OpenJDK Version 1.8.0_352 on Ubuntu for Picard Tool Compatibility

  #1896 opened a year ago by Sadiki-Noureddine
  1

• Picard Cloud

  #1898 opened a year ago by lappazos
  2

• Picard build failed

  #1883 opened a year ago by jiachenli1218
  1

• BUILD FAILED error

  #1874 opened 2 years ago by HK0911
  1